public static bool IsAssemblyFinished(this GenomeModel genomeModel)
{
int assemblersFinished = 0;
if (genomeModel.UseMasurca)
{
if (genomeModel.MasurcaCurrentStep.Equals(StepDescriptions.GetMasurcaStepList().Last().step))
{
assemblersFinished++;
}
}
if (genomeModel.UseSGA)
{
}
if (genomeModel.UseWGS)
{
}
if (assemblersFinished.Equals(genomeModel.NumberOfAssemblers))
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Updates the status of the masurca assembler. If it has either errored out (-1) or is completed (last step), it will not change the status.
/// </summary>
/// <param name="client">The current SSH client session.</param>
/// <param name="genomeModel">The model of the particular job.</param>
private static void CheckMasurcaStep(SshClient client, GenomeModel genomeModel)
{
if (string.IsNullOrEmpty(ErrorHandling.error) &&
!genomeModel.MasurcaCurrentStep.Equals(-1) &&
!genomeModel.MasurcaCurrentStep.Equals(StepDescriptions.GetMasurcaStepList().Last().step))
{
if (LinuxCommands.DirectoryHasFiles(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed)))
{
int currentMasurcaStep = LinuxCommands.GetCurrentStep(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed), StepDescriptions.GetMasurcaStepList());
// Provided we didn't encounter an error, set the status of masurca and the job.
if (currentMasurcaStep != -1)
{
genomeModel.MasurcaCurrentStep = currentMasurcaStep;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), currentMasurcaStep);
}
else
{
StepDescriptions.SetMasurcaError(client, genomeModel);
}
}
// Either masurca hasn't started or it has but no files have been created yet.
else
{
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
}
}
}
/// <summary>
/// Sets default values if the user decided not to enter any information for optional values in the wizard.
/// </summary>
/// <param name="genomeModel">The model data for a particular job.</param>
/// <returns>Returns the new job model with the default values.</returns>
public static GenomeModel SetDefaultMasurcaValues(GenomeModel genomeModel)
{
// If they don't have jump reads.
if (genomeModel.JumpReads == false)
{
genomeModel.JumpLength = 0;
}
// If they don't have paired-end reads.
if (genomeModel.PEReads == false)
{
genomeModel.PairedEndLength = 0;
}
if (genomeModel.MasurcaMean == null)
{
genomeModel.MasurcaMean = 180;
}
if (genomeModel.MasurcaStdev == null)
{
genomeModel.MasurcaStdev = 20;
}
// We don't specify anything here. If it is null, we set it to AUTO in the masurca method of the config builder.
if (genomeModel.MasurcaGraphKMerValue == null)
{
if (genomeModel.MasurcaKMerErrorCount == null)
{
genomeModel.MasurcaKMerErrorCount = 1;
}
}
if (genomeModel.MasurcaThreadNum == null)
{
genomeModel.MasurcaThreadNum = 20;
}
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
return(genomeModel);
}
/// <summary>
/// Updates the status of a single job. But it does not perform the upload if that needs to happen.
/// </summary>
/// <param name="genomeModel">The model of the particular job.</param>
protected internal static void UpdateStatus(GenomeModel genomeModel)
{
using (var client = new SshClient(CreatePrivateKeyConnectionInfo()))
{
try
{
client.Connect();
/// TODO: Modify the code to skip entire sections if they have already been completed. This will be based off the CURRENT STEP stored in the model data.
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
bool continueUpdate = true; // Determines whether we will continue checking the job status.
bool DEBUG_MODE = false; // Debug mode to skip some assembler steps.
bool outOfRange = false; // If the overall step is out of bounds, then we set this to true to attempt a correction.
ErrorHandling.error = ""; // Reset the errror flag.
while (continueUpdate && ErrorHandling.NoError())
{
// Depending on the current step, this switch will determine if the state of the job needs to change.
switch (genomeModel.OverallCurrentStep)
{
// Queued step
case 1:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (LinuxCommands.IsProcessRunning(client, "conversionScript.sh"))
{
genomeModel.NextStep();
}
// If a conversion was never run or if we missed it, then check if the job has already started.
else if (LinuxCommands.JobRunningAlt(client, genomeModel.SSHUser))
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Data conversion step
case 2:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (LinuxCommands.DirectoryHasFiles(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed)))
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Running assemblers step
case 3:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (genomeModel.UseMasurca)
{
CheckMasurcaStep(client, genomeModel);
}
if (genomeModel.UseSGA)
{
}
if (genomeModel.UseWGS)
{
}
if (genomeModel.IsAssemblyFinished())
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Data analysis step
case 4:
{
// Until data analysis is implemented, we skip the step.
genomeModel.NextStep();
break;
//if (LinuxCommands.IsProcessRunning(client, "dataAnalysis.sh"))
// continueUpdate = false;
//else
//{
// // Has it finished?
// if (LinuxCommands.FileExists(client, Accessors.GetJobOutputPath(genomeModel.Seed) + "dataAnalysisResult"))
// genomeModel.NextStep();
// else
// LinuxCommands.RunDataAnalysis(client);
//}
//break;
}
// TODO: Create a more robust method in checking for a completed upload. Maybe connect to the FTP and compare file sizes and see if they are close.
// Uploading Data step
case 5:
{
//if (LinuxCommands.IsJobUploading(client, Accessors.USER_ROOT_JOB_DIRECTORY, Accessors.GetCompressedDataPath(genomeModel.Seed)))
// continueUpdate = false;
//else if (LinuxCommands.FileExists(client, Accessors.GetCompressedDataPath(genomeModel.Seed)))
// genomeModel.NextStep();
//else
//{
LinuxCommands.UploadJobData(client, Accessors.USER_ROOT_JOB_DIRECTORY, Accessors.GetCompressedDataPath(genomeModel.Seed)
, Accessors.GetRelativeJobDirectory(genomeModel.Seed), Accessors.GetRemoteDownloadLocation(genomeModel.Seed), true, "yr");
continueUpdate = false;
//}
break;
}
// Completed step
case 6:
{
continueUpdate = false;
break;
}
default:
{
// If we have attempted a correction and failed, throw in the towel.
if (outOfRange)
{
throw new IndexOutOfRangeException("The current step of the program is out of bounds after an attempted correction. The current step: "
+ genomeModel.OverallCurrentStep);
}
else
{
outOfRange = true;
// Reset the state to default and have it run through the update method again.
genomeModel.OverallCurrentStep = 1;
genomeModel.OverallStatus = StepDescriptions.GetOverallStepList()[genomeModel.OverallCurrentStep].ToString();
}
break;
}
}
}
}
}
// SSH Connection couldn't be established.
catch (SocketException e)
{
ErrorHandling.error = "The SSH connection couldn't be established. " + e.Message;
}
// The SSH connection was dropped.
catch (SshConnectionException e)
{
ErrorHandling.error = "The connection was terminated unexpectedly. " + e.Message;
}
}
}
