public bool Notify(GNAnalysisRequest analysisRequest)
{
LogUtil.LogMethod(logger, MethodBase.GetCurrentMethod());
try
{
GNCloudFile GNCloudVCF = (from a in analysisRequest.AnalysisResult.ResultFiles
where a.GNCloudFileCategoryId == 2
select a).FirstOrDefault <GNCloudFile>();
GNNewSampleBatch batch = analysisRequest.GNAnalysisRequestGNSamples.FirstOrDefault().GNSample.GNNewSampleBatchSample.GNNewSampleBatch;
AnalysisCompletionMessage message = new AnalysisCompletionMessage
{
analysisId = analysisRequest.Id.ToString(),
batchId = batch.BatchId,
project = batch.Project,
repository = batch.Repository,
bamViewerURL = "https://secure.genomenext.net/GNPortal-1.3/AnalysisRequests/BamViewer?analysisId=" + analysisRequest.Id.ToString(),
vcfFilename = GNCloudVCF.FileURL.Replace("https://", "s3://").Replace(".s3.amazonaws.com", "")
};
System.Console.WriteLine("***\n ****** Sending message " + analysisRequest.CreateDateTime);
this.SendMessage(message);
}
catch (Exception e1)
{
System.Console.WriteLine("***\n ****** Exception Sending message " + e1.InnerException + e1.Message + e1.StackTrace);
Exception e2 = new Exception("Unable to send notification to queue.", e1);
LogUtil.Warn(logger, e2.Message, e2);
return(false);
}
return(true);
}
public async Task <bool> ProcessQCMessage(NewSampleBatchStatus newSampleMessageStatus)
{
System.Console.WriteLine("QCQCQC " + newSampleMessageStatus.name);
try
{
GNCloudFileCategory fileCategory = db.GNCloudFileCategories.Where(a => a.Id == 1).FirstOrDefault();
string sampleName1 = newSampleMessageStatus.name;
string sampleName = sampleName1.Substring(0, sampleName1.IndexOf("_"));
//s3://sanford-fastq/151204_SN7001383_0164_AC7Y91ACXX/FASTQ/fastqc/AAA076960/AAA076960_S6_R2_001/
GNSample sample = db.GNSamples.Where(a => a.Name.Equals(sampleName) && a.IsReady == false).FirstOrDefault();
GNCloudStorageService st = new GNCloudStorageService();
string volume = "dev-gn-s3-01";
Guid fileId = Guid.NewGuid();
string folderPath = "fastq/" + sample.Id + "/" + fileId + "/";
string fastqFileName = folderPath + newSampleMessageStatus.name + ".fastq.gz";
string fileURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + fastqFileName;
string originBucket = newSampleMessageStatus.filesBucket;
originBucket = originBucket.Replace("s3://", "");
originBucket = originBucket.Substring(0, originBucket.IndexOf("/")); //"sanford-fastq";
string QcOriginKey = newSampleMessageStatus.filesBucket;
QcOriginKey = QcOriginKey.Replace("s3://", "");
QcOriginKey = QcOriginKey.Substring(originBucket.Length + 1);
string FileDescription = newSampleMessageStatus.name + ".fastq.gz";
string fastqOriginKey = QcOriginKey.Substring(0, QcOriginKey.IndexOf("FASTQ/") + 5);
fastqOriginKey = fastqOriginKey + "/" + FileDescription;
QcOriginKey = QcOriginKey + "fastqc_report.html";
string destinationBucket = "dev-gn-s3-01/" + folderPath;
destinationBucket = "dev-gn-s3-01";
string QcFileName = folderPath + "fastqc_report.html";
string QcDestinationURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + QcFileName;
st.CopyS3Object(originBucket, fastqOriginKey, destinationBucket, fastqFileName);
st.CopyS3Object(originBucket, QcOriginKey, destinationBucket, QcFileName);
GNCloudFile cloudFile = new GNCloudFile
{
Id = fileId,
GNCloudFileCategoryId = fileCategory.Id, //FASTQ
CloudFileCategory = fileCategory,
FileName = folderPath + fastqFileName,
FileURL = fileURL,
FolderPath = folderPath,
Volume = volume,
Description = fastqFileName,
FileSize = st.GetObjectSize(originBucket, fastqOriginKey),
AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName,
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
SampleId = sample.Id.ToString(),
PassedQC = (newSampleMessageStatus.isError.Equals("false")),
QcReportLocation = QcDestinationURL
};
db.GNCloudFiles.Add(cloudFile);
sample.CloudFiles.Add(cloudFile);
if (sample.CloudFiles.Count() == 2 && sample.CloudFiles.Where(a => a.PassedQC == false).Count() == 0)
{
sample.IsReady = true;
if (sample.GNNewSampleBatchSample.GNNewSampleBatch.AutoStartAnalysis)
{
GNAnalysisRequest analysis = sample.GNAnalysisRequestGNSamples.FirstOrDefault().GNAnalysisRequest;
AnalysisRequestService analysisService = new AnalysisRequestService(db);
GNContact userContact = db.GNContacts.Find(Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"));
await analysisService.StartAnalysis(userContact, analysis.Id);
}
}
db.SaveChanges();
}
catch (Exception e)
{
System.Console.WriteLine("***Unable to Update QC-COMPLETED status. " + e.Message + e.StackTrace + " **********************************");
Exception e2 = new Exception("Unable to Update QC-COMPLETED status.", e);
LogUtil.Warn(logger, e2.Message, e2);
return(false);
}
return(true);
}
/**
* JSON Format
*/
public void PrepareBamViewer(GNAnalysisRequest analysisRequest)
{
GNCloudFile GNCloudVCF = (from a in analysisRequest.AnalysisResult.ResultFiles
where a.GNCloudFileCategoryId == 2
select a).FirstOrDefault <GNCloudFile>();
string vcfFilePath = GNCloudVCF.FileURL.Substring(0, GNCloudVCF.Description.LastIndexOf('/'));
string vcfFile = GNCloudVCF.Description.Substring(GNCloudVCF.Description.LastIndexOf('/') + 1);
string fileContents = "";
//List<string>.Enumerator enumerator = samplesSelected.GetEnumerator();
BamConfigFile bamRequest = new BamConfigFile();
bamRequest.analysisId = analysisRequest.Id.ToString();
bamRequest.analysisDescription = analysisRequest.Description;
bamRequest.vcfFilename = vcfFile;
bamRequest.listOfSamples = new List <AnalysisResultSample>();
bamRequest.totalNumberOfSamples = analysisRequest.GNAnalysisRequestGNSamples.Count();
try
{
int lineNum = 0;
foreach (GNAnalysisRequestGNSample analysisSampleInput in analysisRequest.GNAnalysisRequestGNSamples)
{
lineNum++;
GNSample sampleInput = analysisSampleInput.GNSample;
string sampleInputName = sampleInput.Name;
sampleInputName = sampleInputName.Replace(" ", "_").Replace("(", "_").Replace(")", "_").ToUpper();
string baiFile = analysisRequest.AnalysisResult.ResultFiles.Where(a => a.FileName.Contains(sampleInputName) && a.FileName.Contains("bai")).FirstOrDefault().FileName;
string bamFile = analysisRequest.AnalysisResult.ResultFiles.Where(a => a.FileName.Contains(sampleInputName) && a.FileName.Contains("bam") && !a.FileName.Contains("bai")).FirstOrDefault().FileName;
string item = bamFile + " " + baiFile + " " + analysisRequest.Id.ToString() + " " + vcfFile + " " + sampleInput.Name + " " + lineNum + " " + analysisRequest.Description.Replace(" ", "_").Trim().ToUpper();
fileContents = fileContents + item + "\n";
// await this.transactionService.CreateBillingTransactionsPerAnalysisSample(userContact, analysisRequest, analysisRequest.AnalysisType.Name, analysisRequest.Description, false, false, "REPORT_BAM_VIEWER", sampleInput);
bamRequest.listOfSamples.Add(new AnalysisResultSample
{
index = lineNum,
sampleId = sampleInput.Id.ToString(),
name = sampleInputName,
baiFilename = baiFile,
bamFilename = bamFile
}
);
}
}
catch (Exception e)
{
logger.Error("Error while launching BAM Viewer " + e.Message);
}
GNNewSampleBatch batch = analysisRequest.GNAnalysisRequestGNSamples.FirstOrDefault().GNSample.GNNewSampleBatchSample.GNNewSampleBatch;
BamViewerRequest bamViewerRequest = new BamViewerRequest {
bamViewerURL = vcfFilePath,
batchId = batch.BatchId,
organization = batch.GNSequencerJob.GNOrganization.Name,
project = batch.GNSequencerJob.Project,
repository = batch.Repository,
vcfFilepath = vcfFilePath,
bamConfigFile = bamRequest
};
try
{
System.Console.WriteLine("***\n ****** Sending message ");
this.SendMessage(bamViewerRequest);
}
catch (Exception exception)
{
logger.Error(exception.Message);
throw;
}
}
public override bool ProcessMessage(QcReport qcReportSqsMessage, object queueMessage)
{
System.Console.WriteLine("***\n ****** Sample Name: " + qcReportSqsMessage.entityID);
System.Console.WriteLine("***\n ****** Sample type: " + qcReportSqsMessage.entityType);
System.Console.WriteLine("***\n ---->QC REPORT PROCESSING FOR ENTITY: " + qcReportSqsMessage.entityID + " (" + qcReportSqsMessage.entityType + ")");
/**
* Find Sample in NewSamplesBatch
*
*/
bool success = false;
try
{
Guid entityId = Guid.Parse(qcReportSqsMessage.entityID);
if (qcReportSqsMessage.entityType.ToUpper().Equals("SAMPLE"))
{
GNSample sample = db.GNSamples.Find(entityId);
//Find Batch
//GNNewSampleBatch Batch = db.GNNewSampleBatchSamples.Where(a => a.GNSample.Id.Equals(sample.Id)).FirstOrDefault().GNNewSampleBatch;
System.Console.WriteLine("***\n ----> SAMPLE FOUND: " + sample.Name);
GNCloudFileCategory fileCategory = db.GNCloudFileCategories.Where(a => a.Id == 1).FirstOrDefault();
string description = qcReportSqsMessage.fileName;
string volume = "dev-gn-s3-01";
string folderPath = qcReportSqsMessage.fileLocation.Substring(qcReportSqsMessage.fileLocation.IndexOf("fastq/"));
string fileURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + folderPath + description;
System.Console.WriteLine("***\n ----> fileURL: " + fileURL);
//check first if file already exists
int cloudFileExists = db.GNCloudFiles.Where(a => a.FileURL.Equals(fileURL)).Count();
System.Console.WriteLine("\n\n\n ----> FILE EXISTS?: " + cloudFileExists + " - " + sample.Id + " - " + fileURL);
//if not, insert
if (cloudFileExists == 0)
{
GNCloudFile cloudFile = new GNCloudFile
{
Id = Guid.NewGuid(),
GNCloudFileCategoryId = fileCategory.Id, //FASTQ
CloudFileCategory = fileCategory,
FileName = folderPath + description,
FileURL = fileURL,
FolderPath = folderPath,
Volume = volume,
Description = description,
FileSize = Int64.Parse(qcReportSqsMessage.fileSize) * 1024,
AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName,
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
SampleId = sample.Id.ToString(),
QcStatsAvailable = (qcReportSqsMessage.qcResult.Equals("true")),
QcStatsReportLocation = qcReportSqsMessage.qcReportLocation
};
db.GNCloudFiles.Add(cloudFile);
sample.CloudFiles.Add(cloudFile);
System.Console.WriteLine("***\n ----> FILE ADDED TO SAMPLE: " + cloudFile.Id);
/*
* Batch.TotalNumberOfFastqFilesCompleted = Batch.TotalNumberOfFastqFilesCompleted + 1;
*
* if (Batch.TotalNumberOfFastqFiles == Batch.TotalNumberOfFastqFilesCompleted)
* {
* SampleBatchRequestService batchService = new SampleBatchRequestService();
* batchService.QualityControl(Batch);
* }*/
}
}
else
{
//Update VCF-QC for an existing VCF
System.Console.WriteLine("***\n ****** UPDATING ANALYSIS : " + qcReportSqsMessage.entityID);
System.Console.WriteLine("***\n ****** " + qcReportSqsMessage.entityType);
GNAnalysisRequest analysisRequest = db.GNAnalysisRequests.Find(entityId);
System.Console.WriteLine("***\n ****** CreateDateTime" + analysisRequest.CreateDateTime);
GNCloudFile vcfFile = analysisRequest.AnalysisResult.ResultFiles.Where(a => a.FileName.Contains(qcReportSqsMessage.fileName)).FirstOrDefault();
System.Console.WriteLine("***\n ****** File found " + vcfFile.FileURL);
vcfFile.QcStatsReportLocation = qcReportSqsMessage.qcReportLocation;
vcfFile.QcStatsAvailable = true;
System.Console.WriteLine("***\n ----> Analysis Request: " + analysisRequest.Description);
System.Console.WriteLine("***\n ----> VCF File Found: " + vcfFile.Description);
}
db.SaveChanges();
success = true;
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to process QCReport Message.", e1);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
