private async Task AssignToChannel(OligoSynthesisActivity currentSynthesisActivity, IEnumerable <OligoSynthesisActivity> otherSynthesisActivities)
{
IEnumerable <ChannelConfigurationItemViewModel> allChannels = await channelConfigurationService.GetChannelConfigurations();
if (allChannels.Any(x => x.ChannelNumber == currentSynthesisActivity.ChannelNumber &&
currentSynthesisActivity.DNASequence.StartsWith(x.StartNucleotide)))
{
return;
}
currentSynthesisActivity.ChannelNumber = 0;
IEnumerable <ChannelConfigurationItemViewModel> availableChannels =
allChannels.Where(x => currentSynthesisActivity.DNASequence.StartsWith(x.StartNucleotide));
foreach (ChannelConfigurationItemViewModel availableChannelConfiguration in availableChannels)
{
if (otherSynthesisActivities.All(x => x.ChannelNumber != availableChannelConfiguration.ChannelNumber))
{
currentSynthesisActivity.ChannelNumber = availableChannelConfiguration.ChannelNumber;
currentSynthesisActivity.ChannelApiFunction = unitOfWork.GetById <HardwareFunction>(availableChannelConfiguration.HardwareFunction.Id);
}
}
if (currentSynthesisActivity.ChannelNumber < 1)
{
throw new Exception(string.Format(AppResources.ChannelNotConfigured, currentSynthesisActivity.DNASequence[0]));
}
}
public OligoSynthesisActivity CreateOligoSynthesisActivity()
{
OligoSynthesisActivity oligoSynthesisActivity = new OligoSynthesisActivity()
{
DNASequence = "GG",
OligoSynthesisProcess = CreateOligoSynthesisProcess(),
SynthesisCycle = CreateSynthesisCycle(),
ChannelApiFunction = CreateHardwareFunction(),
};
return(GetOrCreate(() => oligoSynthesisActivity));
}
public async Task CreateOrUpdateSynthesisActivity(SynthesisActivityItemViewModel item)
{
OligoSynthesisActivity entity;
OligoSynthesisProcess currentOligoSynthesisProcess = await GetCurrentOligoSynthesisProcess();
if (string.IsNullOrWhiteSpace(item.Id))
{
entity = new OligoSynthesisActivity();
entity.OligoSynthesisProcess = currentOligoSynthesisProcess;
}
else
{
entity = currentOligoSynthesisProcess.OligoSynthesisActivities.Single(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>()
.Include(x => x.CycleSteps)
.SingleAsync(x => x.UserId == null);
entity.SynthesisCycle = defaultSynthesisCycle;
}
await AssignToChannel(entity, currentOligoSynthesisProcess.OligoSynthesisActivities);
CalcOligoSynthesisActivityTotalTime(entity);
unitOfWork.InsertOrUpdate(entity);
unitOfWork.Commit();
currentOligoSynthesisProcess = await GetCurrentOligoSynthesisProcess();
currentOligoSynthesisProcess.TotalTime = currentOligoSynthesisProcess.OligoSynthesisActivities.Sum(x => x.TotalTime);
unitOfWork.Commit();
}
private void CalcOligoSynthesisActivityTotalTime(OligoSynthesisActivity oligoSynthesisActivity)
{
string dnaSequence =
oligoSynthesisActivity.DNASequence.Substring(1, oligoSynthesisActivity.DNASequence.Length - 1);
int synthesisActivityTime = 0;
foreach (char nucleotide in dnaSequence.ToCharArray())
{
foreach (CycleStep cycleStep in oligoSynthesisActivity.SynthesisCycle.CycleSteps.OrderBy(x => x.Number))
{
bool isCycleStepApplicable = IsCycleStepApplicable(nucleotide, cycleStep);
if (isCycleStepApplicable)
{
synthesisActivityTime += cycleStep.StepTime;
}
}
}
oligoSynthesisActivity.TotalTime = synthesisActivityTime;
}
public async Task StartSynthesis(OligoSynthesisActivity oligoSynthesisActivity, IEnumerable <HardwareFunction> bAndTetToColFunctions,
HardwareFunction closeAllValvesFunction, int oligoSynthesisActivityTotalTime)
{
try
{
isRunning = true;
if (oligoSynthesisActivity.DNASequence.Length < 2)
{
throw new Exception($"DNA sequence length should be >= 2: {oligoSynthesisActivity.DNASequence}");
}
logAction(
$"Starting oligo synthesis activity. CH '{oligoSynthesisActivity.ChannelNumber}': SEQ '{oligoSynthesisActivity.DNASequence}' : Time '{oligoSynthesisActivityTotalTime} s'");
string dnaSequence =
oligoSynthesisActivity.DNASequence.Substring(1, oligoSynthesisActivity.DNASequence.Length - 1);
await ExecuteHardwareFunction(oligoSynthesisActivity.ChannelApiFunction.ApiUrl);
foreach (char nucleotide in dnaSequence.ToCharArray())
{
foreach (CycleStep cycleStep in oligoSynthesisActivity.SynthesisCycle.CycleSteps.OrderBy(x => x.Number))
{
bool isCycleStepApplicable = IsCycleStepApplicable(nucleotide, cycleStep);
if (isCycleStepApplicable)
{
string cycleStepApiUrl = GetCycleStepApiUrl(cycleStep, nucleotide, bAndTetToColFunctions);
logAction(
$"CH '{oligoSynthesisActivity.ChannelNumber}': SEQ '{oligoSynthesisActivity.DNASequence}': NUC '{nucleotide}' : STEP '{cycleStep.Number}' : TIME: {cycleStep.StepTime} : FUNC '{cycleStepApiUrl}': NAME '{cycleStep.HardwareFunction.Name}'");
await ExecuteHardwareFunction(cycleStepApiUrl);
await Task.Delay(cycleStep.StepTime * 1000);
logAction($"Opened valves: {cycleStep.HardwareFunction.Description}");
await ExecuteHardwareFunction(closeAllValvesFunction.ApiUrl);
oligoSynthesisActivityTotalTime -= cycleStep.StepTime;
logAction($"Remaining time: {oligoSynthesisActivityTotalTime} s ");
if (cycleStep.SafeStep && IsSuspended)
{
logAction("Synthesis suspended");
while (isSuspended)
{
await Task.Delay(100);
}
logAction("Synthesis resumed");
}
if (cycleStep.SafeStep && IsForceStopRequested)
{
ResetStates();
logAction("Synthesis stopped");
return;
}
}
}
}
logAction(
$"Synthesis completed. CH '{oligoSynthesisActivity.ChannelNumber}': SEQ '{oligoSynthesisActivity.DNASequence}'");
}
catch (Exception ex)
{
logAction(
$"Synthesis failed: CH '{oligoSynthesisActivity.ChannelNumber}': SEQ '{oligoSynthesisActivity.DNASequence}'. Message: {ex.Message}");
await ExecuteHardwareFunction(closeAllValvesFunction.ApiUrl);
}
finally
{
ResetStates();
}
}
