/// <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);
}
}
}
protected internal static string GetMasurcaError(SshClient client, int seed)
{
using (var cmd = client.CreateCommand("cat " + Accessors.GetMasurcaFailureLogPath(seed, true)))
{
cmd.Execute();
ErrorHandling.CommandError(cmd);
return(cmd.Result.ToString());
}
}
/// <summary>
/// Creates the initial file which is run at the beginning of each run. The primary function of which is to download the user's data at runtime.
/// </summary>
private void BuildInitConfig()
{
// File Server
string fileName = "init_" + seed + ".sh";
string fullPath = localPath + fileName;
// BigDog
string jobDataDirectory = Accessors.GetJobDataPath(seed);
if (!File.Exists(fullPath))
{
try
{
using (TextWriter tw = new StreamWriter(fullPath))
{
tw.WriteLine("#!/bin/bash");
// Note: Due to the fact that the compute nodes do not have internet access, an ssh to the login node (which does) is required for the
// data to download successfully.
tw.WriteLine("ssh login-0-0");
// If we have sequential reads there will be only a single URL:
if (dataSources.Count == 1)
{
tw.WriteLine("wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 5 -O " + jobDataDirectory + "sequentialData.fastq " + dataSources[0].ToString());
}
// If we have any other type of reads there will be at least a left and right read:
else
{
List <string> leftReads = new List <string>();
List <string> rightReads = new List <string>();
string concatFiles = "";
// Create the URL lists with the left and right reads split.
HelperMethods.CreateUrlLists(dataSources, out leftReads, out rightReads);
// Now add the wgets for the left reads URLs and rename them to leftData_[j]:
for (int j = 0; j < leftReads.Count; j++)
{
string newDataName = "leftData_" + j;
tw.WriteLine("wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 5 -O " + jobDataDirectory + newDataName + " " + leftReads[j].ToString());
// If it is compressed, uncompress the data. Add additional and more concise checks here later.
if (leftReads[j].ToString().Contains(".gz"))
{
tw.WriteLine("gunzip " + newDataName);
}
concatFiles = concatFiles + " " + jobDataDirectory + "leftData_" + j;
}
// Concat the left reads together into a leftReads.fastq file and delete old files.
tw.WriteLine("cat " + concatFiles + " > " + jobDataDirectory + "leftReads.fastq");
tw.WriteLine("rm " + jobDataDirectory + "leftData_*");
concatFiles = "";
// Now add the wgets for the right reads URLs and rename them to rightData_[i]:
for (int i = 0; i < rightReads.Count; i++)
{
string newDataName = "rightData_" + i;
tw.WriteLine("wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 5 -O " + jobDataDirectory + newDataName + " " + rightReads[i].ToString());
// If it is compressed, uncompress the data. Add additional and more concise checks here later.
if (rightReads[i].ToString().Contains(".gz"))
{
tw.WriteLine("gunzip " + newDataName);
}
concatFiles = concatFiles + " " + jobDataDirectory + "rightData_" + i;
}
// Concat the right reads together into a rightReads.fastq file and delete old files.
tw.WriteLine("cat " + concatFiles + " > " + jobDataDirectory + "rightReads.fastq");
tw.WriteLine("rm " + jobDataDirectory + "rightData_* ");
}
// Exit the ssh session for the login node.
tw.WriteLine("exit");
// DEBUG: COMMENTING OUT FOR TESTING PURPOSES.
if (genomeModel.UseMasurca)
{
// Generate assembly file in the output directory because that is where the files will be generated by default.
tw.WriteLine("/share/bio/masurca/bin/masurca " + Accessors.GetMasurcaScriptPath(seed)
+ " -o " + Accessors.GetMasurcaOutputPath(seed) + "assembly.sh");
// Run the assembler.
tw.WriteLine("." + Accessors.GetMasurcaOutputPath(seed) + "assembly.sh");
}
if (genomeModel.UseSGA)
{
}
if (genomeModel.UseWGS)
{
}
tw.WriteLine("#EOF");
InitConfigURL = Accessors.FTP_URL + urlPath + fileName;
}
}
catch (Exception e)
{
ErrorHandling.error = e.Message;
}
}
// We have a problem since the file already exists.
else
{
ErrorHandling.error = "Unfortunately, we couldn't create the necessary configuration files to submit your job. Please contact an administrator.";
throw new IOException("Attempted to create \"" + fullPath + "\" but it already exists so we cannot create the file. Continuing is not advised. ");
}
}
/// <summary>
/// Creates all the necessary folders, downloads the config scripts, and adds the job to the scheduler on BigDog.
/// </summary>
/// <returns>Returns true only if a job gets successfully added to SGE.</returns>
public bool CreateJob()
{
// The init.sh script will contain all the basic logic to download the data and initiate the job on the assembler(s).
using (var client = new SshClient(Accessors.BD_IP, genomeModel.SSHUser, genomeModel.SSHPass))
{
// Set defaults
//Accessors.masterPath = "/share/scratch/bioinfo/" + HelperMethods.GetUsername();
string node = Accessors.BD_COMPUTE_NODE1; // default
string wgetLogParameter = "--output-file=" + Accessors.GetJobLogPath(seed) + "wget.error";
string initPath = Accessors.GetJobConfigPath(seed) + "init.sh";
string masurcaPath = Accessors.GetJobConfigPath(seed) + "masurca_config.txt";
string jobName = HelperMethods.GetUsername() + "-" + seed;
try
{
client.Connect();
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.USER_ROOT_JOB_DIRECTORY, "-p");
}
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.GetJobPath(seed), "-p");
}
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.GetJobDataPath(seed), "-p");
}
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.GetJobConfigPath(seed), "-p");
}
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.GetJobOutputPath(seed), "-p");
}
if (NoError())
{
// Create subdirectories in the output directory to separate the outputs.
if (genomeModel.UseMasurca)
{
LinuxCommands.CreateDirectory(client, Accessors.GetMasurcaOutputPath(seed), "-p");
}
if (genomeModel.UseSGA)
{
LinuxCommands.CreateDirectory(client, Accessors.GetSgaOutputPath(seed), "-p");
}
if (genomeModel.UseWGS)
{
LinuxCommands.CreateDirectory(client, Accessors.GetWgsOutputPath(seed), "-p");
}
}
if (NoError())
{
LinuxCommands.CreateDirectory(client, Accessors.GetJobLogPath(seed), "-p");
}
if (NoError())
{
LinuxCommands.DownloadFile(client, initPath, InitConfigURL, wgetLogParameter);
}
if (NoError())
{
LinuxCommands.RunDos2Unix(client, initPath);
}
if (NoError())
{
LinuxCommands.DownloadFile(client, masurcaPath, MasurcaConfigURL, wgetLogParameter);
}
if (NoError())
{
LinuxCommands.RunDos2Unix(client, masurcaPath);
}
if (NoError())
{
LinuxCommands.ChangePermissions(client, Accessors.GetJobPath(seed), "777", "-R");
}
if (NoError())
{
// So COMPUTENODE2 has a smaller load, we want to use that instead.
if (LinuxCommands.GetNodeLoad(client, Accessors.BD_COMPUTE_NODE1) > LinuxCommands.GetNodeLoad(client, Accessors.BD_COMPUTE_NODE2))
{
node = Accessors.BD_COMPUTE_NODE2;
}
else
{
node = Accessors.BD_COMPUTE_NODE1;
}
}
if (NoError())
{
LinuxCommands.AddJobToScheduler(client, Accessors.GetJobDataPath(seed), Accessors.GetJobLogPath(seed), node, jobName, initPath);
}
if (NoError())
{
genomeModel.SGEJobId = LinuxCommands.SetJobNumber(client, genomeModel.SSHUser, jobName);
}
// There were no errors.
if (NoError())
{
return(true);
}
else
{
return(false);
}
}
// SSH Connection couldn't be established.
catch (SocketException e)
{
ErrorHandling.error = "The SSH connection couldn't be established. " + e.Message;
return(false);
}
// Authentication failure.
catch (SshAuthenticationException e)
{
ErrorHandling.error = "The credentials were entered incorrectly. " + e.Message;
return(false);
}
// The SSH connection was dropped.
catch (SshConnectionException e)
{
ErrorHandling.error = "The connection was terminated unexpectedly. " + e.Message;
return(false);
}
catch (Exception e)
{
ErrorHandling.error = "There was an uncaught exception. " + e.Message;
return(false);
}
}
}
/// <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;
}
}
}