/// <summary>
/// We need to verify that a user has sufficient permissions in order to run the assemblers.
/// </summary>
/// <param name="SSHUser">The SSH username of the user.</param>
/// <param name="SSHPass">The SSH password of the user.</param>
/// <returns>Returns a boolean value representing whether or not they have sufficient permissions.</returns>
public static bool VerifyPermissions(string SSHUser, string SSHPass)
{
using (var client = new SshClient(Accessors.BD_IP, SSHUser, SSHPass))
{
try
{
client.Connect();
LinuxCommands.CreateDirectory(client, Accessors.VERIFY_PERMISSIONS_TEST_DIR);
if (!string.IsNullOrEmpty(ErrorHandling.error))
{
ErrorHandling.error = "You do not have sufficient permissions to write to the proper directories. Please contact the BigDog Linux team about addressing this problem.";
return(false);
}
else
{
// We want to remove the directory we just created as a test. We recursively force the deletion.
LinuxCommands.RemoveFile(client, Accessors.VERIFY_PERMISSIONS_TEST_DIR, "-rf");
return(true);
}
}
// 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>
/// 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);
}
}
}
