public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, false, CanvasCoverageMode.TruncatedDynamicRange, 100, CommonOptions.CustomParams);
var callset = GetCallset();
logger.Info($"Normal Vcf path: {callset.NormalVcfPath}");
runner.CallSample(callset);
}
public WorkDayDetailViewModelBase(IWorkManager workManager)
{
_workManager = workManager;
_workManager.DayUpdatedEvent += DayUpdated;
Device.StartTimer(TimeSpan.FromMilliseconds(250), TimerTick);
}
public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, true, CanvasCoverageMode.GCContentWeighted, 300, CommonOptions.CustomParams);
var callset = GetCallset(logger);
runner.CallSample(callset);
}
public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager, IFileLocation runtimeExecutable)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, runtimeExecutable, true, CanvasCoverageMode.GCContentWeighted, 100, CommonOptions.CustomParams);
var callset = GetCallset();
runner.CallSample(callset);
}
public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager, IFileLocation runtimeExecutable)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, runtimeExecutable, false, CanvasCoverageMode.TruncatedDynamicRange, 100, CommonOptions.CustomParams);
var callset = GetCallset();
var spwWorkflow = new SmallPedigreeWorkflow(runner);
spwWorkflow.CallPedigree(callset);
}
public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, false, CanvasCoverageMode.TruncatedDynamicRange, 100, CommonOptions.CustomParams);
var callset = GetCallset();
logger.Info($"Normal Vcf path: {callset.NormalVcfPath}");
runner.CallSample(callset);
}
public HistoryViewModel(IWorkManager workManager, IDataService dataService)
{
_workManager = workManager;
_dataService = dataService;
_dataService.WeekAddedEvent += WeekAdded;
Task.Run(async() => await GetData());
}
public LocationService(IPermissions permissions, IGeolocator geolocator, IWorkManager workManager, ISettingStorage settingStorage, IVibrate vibrate,
ILocalNotifications localNotifications)
{
_permissions = permissions;
_geolocator = geolocator;
_workManager = workManager;
_settingStorage = settingStorage;
_vibrate = vibrate;
_localNotifications = localNotifications;
}
/// <summary>
/// Creates CommunicationServer instance.
/// </summary>
/// <param name="config">Server configuration.</param>
public CommunicationServer(ServerConfig config)
{
// TODO Communication server should be a backup by default. Some work is needed here.
Config = config;
_componentOverseer = new ComponentOverseer(Config.CommunicationTimeout, ComponentOverseerCheckInterval);
_workManager = new WorkManager(_componentOverseer);
_msgProcessor = new MessageProcessor(_componentOverseer, _workManager);
_tcpServer = new TcpServer(Config.Address, _msgProcessor);
}
public SeriesProcessor(IWorkManager <TWorkItem> workManager,
IProgressive progressReporter,
IBufferManager <TWorkItem> bufferManager, IDataSubscribable <TWorkItem> input)
: base(progressReporter, bufferManager, workManager)
{
WorkManager = workManager;
BufferManager = bufferManager;
DataInput = input;
DataInput?.AddSubscriber(this);
}
/// <summary>
/// Creates CommunicationServer instance.
/// </summary>
/// <param name="config">Server configuration.</param>
public CommunicationServer(ServerConfig config)
{
// TODO Communication server should be a backup by default. Some work is needed here.
Config = config;
_componentOverseer = new ComponentOverseer(Config.CommunicationTimeout, ComponentOverseerCheckInterval);
_workManager = new WorkManager(_componentOverseer);
_msgProcessor = new MessageProcessor(_componentOverseer, _workManager);
_tcpServer = new TcpServer(Config.Address, _msgProcessor);
}
public MessageProcessorTests()
{
var serializer = new MessageSerializer();
var validator = new MessageValidator();
_marshaller = new Marshaller(serializer, validator);
_overseer = new ComponentOverseer(5, 1);
_workManager = new WorkManager(_overseer);
_processor = new MessageProcessor(_overseer, _workManager);
}
private IWorker Build <TWorkItem>(IWorkManager <TWorkItem> distrib,
IWorker <TWorkItem> worker, Func <IBufferManager <TWorkItem> > getBufferManager)
{
var buffer = getBufferManager();
var progress = GetProgressReporter(worker, buffer);
var chainingTo = GetDataSource <TWorkItem>();
var newSeries = new SeriesProcessor <TWorkItem>(distrib,
progress, buffer, chainingTo);
return(newSeries);
}
public CanvasRunner(ILogger logger, IWorkManager workManager, ICheckpointRunner checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode,
int countsPerBin, Dictionary<string, string> customParameters = null)
{
_logger = logger;
_workManager = workManager;
_checkpointRunner = checkpointRunner;
_isSomatic = isSomatic;
_canvasFolder = Path.Combine(Utilities.GetAssemblyFolder(typeof(CanvasRunner)));
_coverageMode = coverageMode;
_countsPerBin = countsPerBin;
if (customParameters != null) { _customParameters = customParameters; }
}
public MessageProcessorTests()
{
var serializer = new MessageSerializer();
var validator = new MessageValidator();
_marshaller = new Marshaller(serializer, validator);
_overseer = new ComponentOverseer(5, 1);
_workManager = new WorkManager(_overseer);
_processor = new MessageProcessor(_overseer, _workManager);
}
public SmallPedigreeCheckpointFactory(
ISampleSettings sampleSettings,
IWorkManager workManager,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault, IFileLocation pedigreefileNameStub)
{
_workManager = workManager;
_logger = logger;
_executableProcessor = executableProcessor;
_pedigreefileNameStub = pedigreefileNameStub;
_canvasWorkerFactory = new CanvasWorkerFactory(sampleSettings, workManager, logger, executableProcessor, dbSnpVcfProcessor, detectCnvDefault);
}
public CanvasRunner(ILogger logger, IWorkManager workManager, ICheckpointRunnerAsync checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode,
int countsPerBin, Dictionary <string, string> customParameters = null)
{
_logger = logger;
_workManager = workManager;
_checkpointRunner = checkpointRunner;
_isSomatic = isSomatic;
_canvasFolder = Path.Combine(Utilities.GetAssemblyFolder(typeof(CanvasRunner)));
_coverageMode = coverageMode;
_countsPerBin = countsPerBin;
if (customParameters != null)
{
_customParameters = new Dictionary <string, string>(customParameters, StringComparer.InvariantCultureIgnoreCase);
}
}
public CanvasWorkerFactory(
ISampleSettings sampleSettings,
IWorkManager workManager,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault)
{
_workManager = workManager;
_sampleSettings = sampleSettings;
_logger = logger;
_executableProcessor = executableProcessor;
_dbSnpVcfProcessor = dbSnpVcfProcessor;
_detectCnvDefault = detectCnvDefault;
}
public CanvasEnrichmentCnvCaller(IWorkManager workManager, ILogger logger, IFileLocation canvasExe, IFileLocation runtimeExecutable,
ICanvasAnnotationFileProvider annotationFileProvider,
ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder,
CanvasEnrichmentInputCreator <CanvasEnrichmentInput> enrichmentInputCreator,
CanvasPloidyBedCreator canvasPloidyBedCreator)
{
_workManager = workManager;
_logger = logger;
_canvasExe = canvasExe;
_runtimeExecutable = runtimeExecutable;
_annotationFileProvider = annotationFileProvider;
_singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder;
_enrichmentInputCreator = enrichmentInputCreator;
_canvasPloidyBedCreator = canvasPloidyBedCreator;
}
public CanvasSmallPedigreeWrapper(
IWorkManager workManager,
ILogger logger,
IFileLocation canvasExe, IFileLocation runtimeExecutable,
ICanvasAnnotationFileProvider annotationFileProvider,
ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder,
CanvasPloidyVcfCreator canvasPloidyVcfCreator)
{
_workManager = workManager;
_logger = logger;
_canvasExe = canvasExe;
_annotationFileProvider = annotationFileProvider;
_singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder;
_canvasPloidyVcfCreator = canvasPloidyVcfCreator;
_runtimeExecutable = runtimeExecutable;
}
/// <summary>
/// Creates MessageProcessor instance.
/// </summary>
/// <param name="componentOverseer">Component overseer module.</param>
/// <param name="workManager">Work manager to get work from.</param>
public MessageProcessor(IComponentOverseer componentOverseer, IWorkManager workManager)
{
if (componentOverseer == null)
throw new ArgumentNullException("IComponentOverseer dependancy is null.");
if (workManager == null)
throw new ArgumentNullException("IWorkManager dependancy is null.");
_inputDataQueue = new RawDataQueue();
var serializer = new MessageSerializer();
var validator = new MessageValidator();
_marshaller = new Marshaller(serializer, validator);
_componentOverseer = componentOverseer;
_workManager = workManager;
_processingLock = new AutoResetEvent(false);
}
static int Main(string[] args)
{
Console.WriteLine(Help());
try
{
args = Console.ReadLine().Split(' ');
ArgsValidation(args);
var discName = new string(args[2].Take(2).ToArray());
switch (args[0].ToLower())
{
case "compress":
reader = new FileReader();
writer = new FileWriter();
archivator = new Compressor(reader.GetQueue(), writer.GetQueue());
perfomance = new DiscPerfomanceCounter(discName);
zipper = new WorkManager(args[1], args[2], reader, writer, archivator, perfomance);
break;
case "decompress":
reader = new GZipReader();
writer = new GZipWriter();
archivator = new Decompressor(reader.GetQueue(), writer.GetQueue());
perfomance = new DiscPerfomanceCounter(discName);
zipper = new WorkManager(args[1], args[2], reader, writer, archivator, perfomance);
break;
}
reader.Reading += Progress;
zipper.Launch();
Console.ReadKey();
return(zipper.CallBackResult());
}
catch (Exception ex)
{
Console.WriteLine("Обнаружена ошибка!\n Метод: {0}\n Описание ошибки {1}", ex.TargetSite, ex.Message);
Console.ReadKey();
return(0);
}
}
public MainViewModel(IWorkManager workManager) : base(workManager)
{
Task.Run(async() =>
{
try
{
await MvvmNanoIoC.Resolve <IDataService>().Initialize();
var workDay = await _workManager.GetDay(DateTimeOffset.Now.Date);
Device.BeginInvokeOnMainThread(() =>
{
SetDay(workDay);
});
}
catch (Exception ex)
{
Debug.WriteLine(ex);
}
});
}
/// <summary>
/// Creates MessageProcessor instance.
/// </summary>
/// <param name="componentOverseer">Component overseer module.</param>
/// <param name="workManager">Work manager to get work from.</param>
public MessageProcessor(IComponentOverseer componentOverseer, IWorkManager workManager)
{
if (componentOverseer == null)
{
throw new ArgumentNullException("IComponentOverseer dependancy is null.");
}
if (workManager == null)
{
throw new ArgumentNullException("IWorkManager dependancy is null.");
}
_inputDataQueue = new RawDataQueue();
var serializer = new MessageSerializer();
var validator = new MessageValidator();
_marshaller = new Marshaller(serializer, validator);
_componentOverseer = componentOverseer;
_workManager = workManager;
_processingLock = new AutoResetEvent(false);
}
public StudentsController()
{
_workManager = new WorkManager.Work.WorkManager();
}
public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, true, CanvasCoverageMode.GCContentWeighted, 100, CommonOptions.CustomParams);
var callset = GetCallset();
runner.CallSample(callset);
}
public WorkDayDetailViewModel(IWorkManager workManager) : base(workManager)
{
}
public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager)
{
CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, true, CanvasCoverageMode.TruncatedDynamicRange, 300, CommonOptions.CustomParams);
var callset = GetCallset(logger);
runner.CallSample(callset);
}
public CanvasPloidyBedCreator(ILogger logger, IWorkManager workManager, PloidyCorrector ploidyFixer)
{
_logger = logger;
_workManager = workManager;
_ploidyFixer = ploidyFixer;
}
