private void DoBLAST(string filename)
{
// Update progress bar, set content of user control to initial state
// Load protein sequences
FastaParser parser = new FastaParser();
IList<ISequence> queryList = parser.Parse(filename).ToList();
// Initialize and populate queue of query sequences
Queue<QueueSequence> queryQueue = new Queue<QueueSequence>();
int j = 0; // For debuging
int progValue = 0;
int currentProgress = 0;
foreach (ISequence protein in queryList)
{
QueueSequence qp = new QueueSequence();
qp.Sequence = protein;
qp.Position = j;
string name = j.ToString();
j++;
if (File.Exists(Up.ProjectDir + "\\xml\\" + name + ".xml"))
{
IList<BlastResult> blastResults;
BlastXmlParser parser2 = new BlastXmlParser();
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
progValue = Convert.ToInt32(Math.Round((double)currentProgress / queryList.Count() * 100, 0));
UpdateProgressBar(progValue, "Validating BLAST results.");
currentProgress++;
}
catch
{
queryQueue.Enqueue(qp);
}
}
else
{
queryQueue.Enqueue(qp);
}
}
// Initialize BLAST queue positions to having no jobs (EMPTY)
BlastQueue blastQueue = new BlastQueue();
// While there are proteins left to submit to BLAST, or there are
// busy jobs still on the queue
UpdateProgressBar(progValue, "Starting up BLAST service, please wait.");
while (queryQueue.Count > 0 || blastQueue.isBlastQueueBusy())
{
// Iterate over blastQueue
for (int i = 0; i < BlastQueue.Length; i++)
{
// Get blastJob from array and update status
BlastJob blastJob = blastQueue[i];
QueueSequence qp = new QueueSequence();
qp.Sequence = blastJob.Query;
qp.Position = blastJob.Position;
// if queue position is AVAILABLE
if (blastJob.JobStatus == BlastJob.AVAILABLE)
{
if (queryQueue.Count > 0)
{
QueueSequence qp2 = queryQueue.Dequeue();
// try to submit job, enqueue back the protein if submission failed.
try
{
blastQueue[i] = submit(qp2);
if (blastQueue[i].JobStatus == BlastJob.FAILED)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp2);
}
else
{
UpdateProgressBar(progValue, "Submitting sequences to NCBI BLAST");
}
}
catch (Exception eee)
{
MessageBox.Show(eee.Message);
}
}
}
else
{
string jobId = blastJob.JobId;
NCBIBlastHandler blastService = blastJob.BlastService;
ServiceRequestInformation info = blastService.GetRequestStatus(jobId);
Thread.Sleep(BlastQueue.RequestDelay);
switch (info.Status)
{
case ServiceRequestStatus.Error:
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
break;
case ServiceRequestStatus.Canceled:
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
break;
case ServiceRequestStatus.Ready:
string result = blastService.GetResult(jobId, blastJob.SearchParams);
string name = blastJob.Position.ToString();
TextWriter tw = new StreamWriter(Up.ProjectDir + "\\xml\\" + name + ".xml");
tw.Write(result);
tw.Close();
Debug.WriteLine("BLAST JOB: " + jobId + " , " + name + " , " + info.StatusInformation);
// Added by VF on Jan, 22, 2013. Catches invalid BLAST records
IList<BlastResult> blastResults;
BlastXmlParser parser2 = new BlastXmlParser();
bool parsePassed = false;
int fetchAttempts = 0;
while (!parsePassed && fetchAttempts < 3)
{
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
parsePassed = true;
Debug.WriteLine("FETCH OK JobId: " + jobId + " InputOrder: " + name + ". This is attempt:" + fetchAttempts.ToString());
}
catch (Exception eee)
{
Debug.WriteLine("Trying to fetch JobId: " + jobId + " InputOrder: " + name + ". This is attempt: " + fetchAttempts.ToString());
parsePassed = false;
result = blastService.GetResult(jobId, blastJob.SearchParams);
TextWriter tw2 = new StreamWriter(Up.ProjectDir + "\\xml\\" + name + ".xml");
tw2.Write(result);
tw2.Close();
fetchAttempts += 1;
}
Thread.Sleep(1000);
}
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
}
catch (Exception eee)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
Debug.WriteLine("REQUEUE of JobId: " + " " + jobId + " InputOrder: " + name + " because max fetch is " + fetchAttempts.ToString());
break;
}
currentProgress += 1;
progValue = Convert.ToInt32(Math.Round((double)currentProgress / queryList.Count() * 100, 0));
UpdateProgressBar(progValue, "Saving");
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
if (queryQueue.Count > 0)
{
QueueSequence qp3 = queryQueue.Dequeue();
try
{
blastQueue[i] = submit(qp3);
if (blastQueue[i].JobStatus == BlastJob.FAILED)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp3);
}
else
{
UpdateProgressBar(progValue, "Submitting sequences to NCBI BLAST");
}
}
catch (Exception eee)
{
MessageBox.Show(eee.Message);
MessageBox.Show("Error creating a jobId for sequence " + qp3.Position);
throw new Exception("Error creating a jobId for sequence" + qp3.Position);
}
}
break;
case ServiceRequestStatus.Queued:
break;
case ServiceRequestStatus.Waiting:
break;
default:
MessageBox.Show("BLAST error " + info.Status + " " + blastJob.JobStatus + " for " + qp.Position);
break;
}
}
}
}
}
/// <summary>
/// A helper method for the BLAST task. Submits a job to BLAST.
/// </summary>
/// <param name="qp"></param>
/// <returns></returns>
private BlastJob submit(QueueSequence qp)
{
// Configure BLAST service
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = Up.BlastUseBrowserProxy;
BlastParameters searchParams = new BlastParameters();
string query = ">" + qp.Sequence.DisplayID + "\n" + qp.Sequence.ToString();
searchParams.Add("Program", Up.BlastProgram);
searchParams.Add("Database", Up.BlastDatabase);
searchParams.Add("GeneticCode", Up.BlastGeneticCode);
searchParams.Add("Expect", "10");
searchParams.Add("Query", query);
// Create BLAST service
NCBIBlastHandler blastService = new NCBIBlastHandler();
blastService.Configuration = configParams;
// Submit BLAST Job
string jobId;
try
{
jobId = blastService.SubmitRequest(qp.Sequence, searchParams);
}
catch(Exception eee)
{
if (eee.Message.Contains("WebException"))
{
ToggleProxy();
}
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
// Make sure job was submitted successfully
ServiceRequestInformation info = blastService.GetRequestStatus(jobId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
//Console.WriteLine("\tError Submitting Job: " + info.Status);
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
Thread.Sleep(BlastQueue.SubmitDelay);
//Console.WriteLine("\tSuccessfully submitted jobId: " + jobId);
// Return a BlastJob, set jobStatus to BUSY
BlastJob blastJob = new BlastJob()
{
JobId = jobId,
SearchParams = searchParams,
ConfigParams = configParams,
BlastService = blastService,
JobStatus = BlastJob.BUSY,
Query = qp.Sequence,
Position = qp.Position
};
return blastJob;
}
