public void TransferData()
{
bool nhsRun;
string[] fields;
SessionOptions sessionOptions = new SessionOptions();
//get run parameters
string runId = Framework.GetRunIdFromRunInfoXml(Path.Combine(localRunDir, @"RunInfo.xml"));
//Parse samplesheet
SampleSheetHeader sampleSheetHeader = new SampleSheetHeader(Path.Combine(localRunDir, @"SampleSheet.csv"));
sampleSheetHeader.Populate();
//write variables to log
Framework.WriteLog(@"Local run directory: " + localRunDir, 0);
Framework.WriteLog(@"Run identifier: " + runId, 0);
Framework.WriteLog(@"Local SampleSheet path: " + Path.Combine(localRunDir, @"SampleSheet.csv"), 0);
Framework.WriteLog(@"Experiment name: " + sampleSheetHeader.getExperimentName, 0);
//determine institution
if (sampleSheetHeader.getInvestigatorName == null || sampleSheetHeader.getInvestigatorName == "" || !sampleSheetHeader.getInvestigatorName.Contains('-'))
{
throw new InvalidDataException(@"Investigator name field not provided or malformed.");
}
//split investigtor name field
fields = sampleSheetHeader.getInvestigatorName.Split('-');
if (fields[1].ToUpper() == @"CU")
{
nhsRun = false;
Framework.WriteLog(@"Investigator name: " + fields[0], 0);
Framework.WriteLog(@"Institution name: Cardiff University", 0);
sessionOptions.SshHostKeyFingerprint = config.getWotanSshHostKeyFingerprint;
sessionOptions.HostName = config.getWotanHostName;
sessionOptions.UserName = config.getWotanSshUserName;
sessionOptions.SshPrivateKeyPath = config.getWotanSshPrivateKeyPath;
}
else if (fields[1].ToUpper() == @"NHS")
{
nhsRun = true;
Framework.WriteLog(@"Investigator name: " + fields[0], 0);
Framework.WriteLog(@"Institution name: NHS", 0);
sessionOptions.SshHostKeyFingerprint = config.getCvxGenSshHostKeyFingerprint;
sessionOptions.HostName = config.getCvxGenHostName;
sessionOptions.UserName = config.getCvxGenSshUserName;
sessionOptions.SshPrivateKeyPath = config.getCvxGenSshPrivateKeyPath;
}
else
{
throw new InvalidDataException(@"Institute not recognised. CU an NHS are only available options.");
}
//convert metrics into table
Framework.WriteLog(@"Writing SAV table ...", 0);
string savFilePath = Path.Combine(Path.GetTempPath(), runId + @"_SAV.txt");
Framework.CallSequenceAnalysisViewer(savFilePath, localRunDir, config.getSavExePath);
//transfer data to cluster
if (nhsRun)
{
Framework.WriteLog(@"Starting transfer to cvx-gen ...", 0);
using (Session session = new Session())
{
string remotePath;
if (config.getIsMiSeqHost)
{
remotePath = config.getCvxGenRemoteArchivePath + @"/miseq/" + runId;
}
else
{
remotePath = config.getCvxGenRemoteArchivePath + @"/hiseq/" + runId;
}
session.Open(sessionOptions);
Framework.WriteLog(@"Connected!", 0);
TransferOperationResult transferResult;
TransferOptions transferOptions = new TransferOptions();
transferOptions.TransferMode = TransferMode.Binary;
//make remote project directory
Framework.WriteLog(@"Creating remote directory: " + remotePath, 0);
session.CreateDirectory(remotePath);
//transfer run folder to archive
Framework.WriteLog(@"Tranfer started ...", 0);
transferResult = session.PutFiles(localRunDir, remotePath, false, transferOptions);
transferResult.Check(); // Throw on any error
//transfer SAV file
transferResult = session.PutFiles(savFilePath, config.getCvxGenRemoteSAVPath, false, transferOptions);
transferResult.Check(); // Throw on any error
//execute remote function
Framework.WriteLog(@"Execuing post-run command ...", 0);
session.ExecuteCommand(@"bash " + config.getCvxGenRemoteScriptPath + ' ' + remotePath + ' ' + config.getCvxGenRemoteResultsPath + '/' + runId + @" >> ~/runPipeline.log");
}
}
else
{
//TODO transfer to Wotan
}
//write run transfer completion
using (StreamWriter file = new StreamWriter(Path.Combine(localRunDir, @"TransferComplete.txt")))
{
file.WriteLine(@"NGSTransferComplete," + Program.programVersion);
file.Close();
}
}
public void TransferData()
{
bool nhsRun;
string[] fields;
SessionOptions sessionOptions = new SessionOptions();
//get run parameters
string runId = Framework.GetRunIdFromRunInfoXml(Path.Combine(localRunDir, @"RunInfo.xml"));
//Parse samplesheet
SampleSheetHeader sampleSheetHeader = new SampleSheetHeader(Path.Combine(localRunDir, @"SampleSheet.csv"));
sampleSheetHeader.Populate();
//write variables to log
Framework.WriteLog(@"Local run directory: " + localRunDir, 0);
Framework.WriteLog(@"Run identifier: " + runId, 0);
Framework.WriteLog(@"Local SampleSheet path: " + Path.Combine(localRunDir, @"SampleSheet.csv"), 0);
Framework.WriteLog(@"Experiment name: " + sampleSheetHeader.getExperimentName, 0);
//determine institution
if (sampleSheetHeader.getInvestigatorName == null || sampleSheetHeader.getInvestigatorName == "" || !sampleSheetHeader.getInvestigatorName.Contains('-'))
{
throw new InvalidDataException(@"Investigator name field not provided or malformed.");
}
//split investigtor name field
fields = sampleSheetHeader.getInvestigatorName.Split('-');
if (fields[1].ToUpper() == @"CU")
{
nhsRun = false;
Framework.WriteLog(@"Investigator name: " + fields[0], 0);
Framework.WriteLog(@"Institution name: Cardiff University", 0);
sessionOptions.SshHostKeyFingerprint = config.getWotanSshHostKeyFingerprint;
sessionOptions.HostName = config.getWotanHostName;
sessionOptions.UserName = config.getWotanSshUserName;
sessionOptions.SshPrivateKeyPath = config.getWotanSshPrivateKeyPath;
}
else if (fields[1].ToUpper() == @"NHS")
{
nhsRun = true;
Framework.WriteLog(@"Investigator name: " + fields[0], 0);
Framework.WriteLog(@"Institution name: NHS", 0);
sessionOptions.SshHostKeyFingerprint = config.getCvxGenSshHostKeyFingerprint;
sessionOptions.HostName = config.getCvxGenHostName;
sessionOptions.UserName = config.getCvxGenSshUserName;
sessionOptions.SshPrivateKeyPath = config.getCvxGenSshPrivateKeyPath;
}
else
{
throw new InvalidDataException(@"Institute not recognised. CU an NHS are only available options.");
}
//convert metrics into table
Framework.WriteLog(@"Writing SAV table ...", 0);
string savFilePath = Path.Combine(Path.GetTempPath(), runId + @"_SAV.txt");
Framework.CallSequenceAnalysisViewer(savFilePath, localRunDir, config.getSavExePath);
//transfer data to cluster
if (nhsRun)
{
Framework.WriteLog(@"Starting transfer to cvx-gen ...", 0);
using (Session session = new Session())
{
string remotePath;
if (config.getIsMiSeqHost)
{
remotePath = config.getCvxGenRemoteArchivePath + @"/miseq/" + runId;
}
else
{
remotePath = config.getCvxGenRemoteArchivePath + @"/hiseq/" + runId;
}
session.Open(sessionOptions);
Framework.WriteLog(@"Connected!", 0);
TransferOperationResult transferResult;
TransferOptions transferOptions = new TransferOptions();
transferOptions.TransferMode = TransferMode.Binary;
//make remote project directory
Framework.WriteLog(@"Creating remote directory: " + remotePath, 0);
session.CreateDirectory(remotePath);
//transfer run folder to archive
Framework.WriteLog(@"Tranfer started ...", 0);
transferResult = session.PutFiles(localRunDir, remotePath, false, transferOptions);
transferResult.Check(); // Throw on any error
//transfer SAV file
transferResult = session.PutFiles(savFilePath, config.getCvxGenRemoteSAVPath, false, transferOptions);
transferResult.Check(); // Throw on any error
//execute remote function
Framework.WriteLog(@"Execuing post-run command ...", 0);
session.ExecuteCommand(@"bash " + config.getCvxGenRemoteScriptPath + ' ' + remotePath + ' ' + config.getCvxGenRemoteResultsPath + '/' + runId + @" >> ~/runPipeline.log");
}
}
else
{
//TODO transfer to Wotan
}
//write run transfer completion
using (StreamWriter file = new StreamWriter(Path.Combine(localRunDir, @"TransferComplete.txt")))
{
file.WriteLine(@"NGSTransferComplete," + Program.programVersion);
file.Close();
}
}
