private static void GetCurrentAnalysisRequest(ActionExecutingContext filterContext, GNEntityModelContainer db)
{
try
{
GNAnalysisRequest currentAnalysisRequest = null;
string analysisRequestId = filterContext.HttpContext.Request["analysisRequestId"];
if (!string.IsNullOrEmpty(analysisRequestId))
{
currentAnalysisRequest = db.GNAnalysisRequests.Find(Guid.Parse(analysisRequestId));
}
if (currentAnalysisRequest != null)
{
filterContext.Controller.ViewBag.CurrentAnalysisRequest = currentAnalysisRequest;
}
else
{
filterContext.Controller.ViewBag.CurrentAnalysisRequest = null;
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to retrieve Current AnalysisRequest!!", e);
}
}
public override GNSample DetailsOnLoad(GNSample sample)
{
auditResult = audit.LogEvent(UserContact, sample.Id, this.ENTITY, this.Request.UserHostAddress, EVENT_LOAD_DETAILS_UI);
sample.IsValidPairEnded = ((SampleService)entityService).IsValidPairEnded(sample);
sample.IsValidSingleEnded = ((SampleService)entityService).IsValidSingleEnded(sample);
List <GNSampleRelationshipType> RelationshipTypes = db.GNSampleRelationshipTypes.OrderBy(a => a.MaxRelationships).ThenBy(a => a.Name).ToList();
ViewBag.GNSampleRelationshipTypes = new SelectList(RelationshipTypes, "Id", "Name");
if (Request["analysisRequestId"] != null)
{
Guid AnalysisRequestId = Guid.Parse(Request["analysisRequestId"]);
GNAnalysisRequest AnalysisRequest = db.GNAnalysisRequests.Where(a => a.Id.Equals(AnalysisRequestId)).FirstOrDefault();
ViewBag.CurrentAnalysisRequest = AnalysisRequest;
GNProject Project = db.GNProjects.Where(a => a.Id.Equals(AnalysisRequest.GNProjectId)).FirstOrDefault();
ViewBag.CurrentProject = Project;
Guid TeamId = Project.Teams.FirstOrDefault().Id;
GNTeam Team = db.GNTeams.Where(a => a.Id.Equals(TeamId)).FirstOrDefault();
ViewBag.CurrentTeam = Team;
}
return(base.DetailsOnLoad(sample));
}
private static void MarkAnalysisAsFailed(AnalysisRequestService analysisRequestService, GNAnalysisRequest analysisRequest)
{
if (MARK_ANALYSIS_IN_ERROR_FEATURE_ACTIVE)
{
try
{
//get analysis request from db
GNAnalysisRequest ar = analysisRequestService.db.GNAnalysisRequests
.Include(a => a.AnalysisType)
.Include(a => a.AnalysisStatus)
.Include(a => a.AnalysisResult)
.Where(a => a.Id == analysisRequest.Id)
.FirstOrDefault();
//mark analysis as failed
if (!ar.IsFailedRequest)
{
LogUtil.Info(logger, "Mark Analysis As Failed for AR ID [" + ar.Id + "]...");
System.Console.WriteLine("\nMark Analysis As Failed for AR ID [" + ar.Id + "]...");
analysisRequestService.MarkAnalysisAsFailed(analysisRequestService, ar);
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to Process Failure of Analysis " + analysisRequest.Id + " : " + e.Message, e);
}
}
}
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> AutostartAnalysis(GNAnalysisRequest analysis)
{
AnalysisRequestService analysisService = new AnalysisRequestService(db);
GNContact userContact = db.GNContacts.Find(Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"));
await analysisService.StartAnalysis(userContact, analysis.Id);
return(true);
}
public async Task <ActionResult> List()
{
PopulateSelectLists();
EvalCanCreate();
Dictionary <string, object> filters = new Dictionary <string, object>();
List <GNTemplate> GNTemplates = new List <GNTemplate>();
if (!string.IsNullOrEmpty(Request["analysisRequestId"]))
{
Guid guidAnalysisRequest = Guid.Parse(Request["analysisRequestId"]);
GNAnalysisRequest AnalysisRequest = db.GNAnalysisRequests.Where(a => a.Id.Equals(guidAnalysisRequest)).FirstOrDefault();
ViewBag.AnalysisRequest = AnalysisRequest;
ViewBag.AnalysisName = AnalysisRequest.Description;
ViewBag.AnalysisRequestId = guidAnalysisRequest;
}
if (!string.IsNullOrEmpty(Request["addSampleRelationship"]))
{
int sampleRel = Int32.Parse(Request["GNSampleRelationshipTypeId"]);
Guid thisSample = Guid.Parse(Request["GNLeftSampleId"]);
int maxRelAllowed = db.GNSampleRelationshipTypes.Where(a => a.Id == sampleRel).Select(b => b.MaxRelationships).FirstOrDefault();
int thisSampleRelIdCount = db.GNSampleRelationships.Where(a => a.GNLeftSampleId.Equals(thisSample) && a.GNSampleRelationshipTypeId == sampleRel).Count();
if (thisSampleRelIdCount < maxRelAllowed)
{
//continue
filters.Add("Gender", db.GNSampleRelationshipTypes.Where(a => a.Id == sampleRel).Select(b => b.Gender).FirstOrDefault());
filters.Add("GNOrganizationId", Request["GNOrganizationId"]);
filters.Add("GNLeftSampleId", Request["GNLeftSampleId"]);
GNTemplates = await this.entityService.FindAll(UserContact, IndexStart(), IndexEnd(), filters);
}
else
{
string sampleRelName = db.GNSampleRelationshipTypes.Where(a => a.Id == sampleRel).Select(b => b.Name).FirstOrDefault();
//return error and return to the Details page
string add_s = "";
if (thisSampleRelIdCount > 1)
{
add_s = "s";
}
ViewBag.PedigreeErrorMessage = "This Sample already has " + thisSampleRelIdCount + " " + sampleRelName.ToLower() + add_s + ", the maximum number allowed.";
GNSample sample = db.GNSamples.Where(a => a.Id.Equals(thisSample)).FirstOrDefault();
}
}
GNTemplates = await this.entityService.FindAll(UserContact, IndexStart(), IndexEnd(), filters);
return(View(GNTemplates));
}
private static void ReStartFailedAnalysis(AnalysisRequestService analysisRequestService, GNAnalysisRequest analysisRequest)
{
if (RESTART_ANALYSIS_FEATURE_ACTIVE)
{
try
{
//get analysis request from db
GNAnalysisRequest ar = analysisRequestService.db.GNAnalysisRequests
.Include(a => a.AnalysisType)
.Include(a => a.GNAnalysisRequestGNSamples.Select(s => s.GNSample).Select(s => s.CloudFiles))
.Include(a => a.AnalysisStatus)
.Include(a => a.AnalysisResult)
.Where(a => a.Id == analysisRequest.Id)
.FirstOrDefault();
//determine if analysis re-start is allowed
ar = analysisRequestService.IsValidSampleSet(ar);
ar.CanReStartAnalysis = analysisRequestService.IsAnalysisRestartAllowed(ar, FORCE_RESTART_ANALYSIS);
//restart analysis
if (ar.CanReStartAnalysis && ar.IsFailedRequest)
{
LogUtil.Info(logger, "Restart Analysis for AR ID [" + ar.Id + "]...");
System.Console.WriteLine("\nRestart Analysis for AR ID [" + ar.Id + "]...");
var t = Task.Run(async delegate
{
var arService = new AnalysisRequestService(new GNEntityModelContainer(), new IdentityModelContainer());
//get user contact
GNContact userContact = arService.db.GNContacts.Find(ar.CreatedBy);
if (arService.analysisRequestPendingCloudMessageService == null || arService.cloudStorageService == null)
{
arService.InitCloudServices(userContact.GNOrganization.AWSConfigId);
}
await arService.StartAnalysis(userContact, ar.Id);
});
}
else
{
LogUtil.Info(logger, "UNABLE to Restart Analysis for AR ID [" + ar.Id + "]...");
System.Console.WriteLine("\nUNABLE to Restart Analysis for AR ID [" + ar.Id + "]...");
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to Process Failure of Analysis " + analysisRequest.Id + " : " + e.Message, e);
}
}
}
public async Task <ActionResult> RemoveFromAnalysisRequest(Guid?id)
{
string analysisRequestId = Request["analysisRequestId"];
bool returnToAnalysis = (string.IsNullOrEmpty(Request["returnToAnalysis"]) ? false : bool.Parse(Request["returnToAnalysis"]));
if (id != null && !string.IsNullOrEmpty(analysisRequestId))
{
int result = await((SampleService)entityService).RemoveSampleFromAnalysisRequest(id, analysisRequestId);
//tfrege 2016.03.21 Check if also a group Id was passed (in which case it's an RNA sample)
if (!string.IsNullOrEmpty(Request["GroupId"]))
{
int result2 = await((SampleService)entityService).RemoveSampleFromAnalysisRequestGroup(id, Guid.Parse(Request["GroupId"]));
}
if (returnToAnalysis)
{
Guid GAnalysisRequestId = Guid.Parse(analysisRequestId);
GNAnalysisRequest analysisRequest = db.GNAnalysisRequests.Where(a => a.Id.Equals(GAnalysisRequestId)).FirstOrDefault();
if (analysisRequest.GNAnalysisRequestTypeCode == "DNA")
{
return(RedirectToAction("Edit", "AnalysisRequests", new { id = analysisRequestId }));
}
else
{
return(RedirectToAction("Details", "AnalysisRequests", new { id = analysisRequestId }));
}
}
else
{
Guid sampleId = Guid.Parse(id.ToString());
auditResult = audit.LogEvent(UserContact, sampleId, this.ENTITY, this.Request.UserHostAddress, "REMOVE_FROM_ANALYSIS " + analysisRequestId.ToString());
int addedSampleTypeId = db.GNSamples.Where(a => a.Id.Equals(sampleId)).FirstOrDefault().GNSampleTypeId;
//return RedirectToAction("List", "Samples", new { analysisRequestId = analysisRequestId, GNSampleTypeId = addedSampleTypeId });
if (!string.IsNullOrEmpty(Request["GroupId"]))
{
return(RedirectToAction("List", "Samples", new { analysisRequestId = analysisRequestId, GNSampleTypeId = addedSampleTypeId, GroupId = Request["GroupId"] }));
}
else
{
return(RedirectToAction("List", "Samples", new { analysisRequestId = analysisRequestId, GNSampleTypeId = addedSampleTypeId }));
}
}
}
ViewBag.AnalysisRequestId = analysisRequestId;
return(View());
}
public bool NotifyQCSystem(GNAnalysisRequest analysisRequest, string bucket, string key)
{
LogUtil.LogMethod(logger, MethodBase.GetCurrentMethod());
string fileLocation = bucket + "/" + key;
string vcfPaths = "s3://" + bucket + "/" + key;
string fileName = key.Substring(key.LastIndexOf("/") + 1);
fileLocation = fileLocation.Substring(0, (fileLocation.LastIndexOf("/")));
try
{
StartVcfStatsReport startStatsReport = new StartVcfStatsReport
{
entityId = analysisRequest.Id.ToString(),
entityType = "ANALYSIS",
fileLocation = fileLocation,
filename = fileName,
vcfPaths = vcfPaths
};
string filename = analysisRequest.Id.ToString() + ".txt";
//string filename = "gn_sample_vcfqc.json";
//System.Threading.Thread.Sleep(5000);
System.Console.WriteLine("***\n ****** Sending message " + analysisRequest.CreateDateTime);
this.SendMessage(startStatsReport);
this.StoreMessage(startStatsReport, "telma.gn.com", filename);
}
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);
}
private static void TerminateInstancesForAnalysis(GNAnalysisRequest analysisRequest)
{
List <Reservation> analysisMasterInstances = null;
List <Reservation> analysisWorkerInstances = null;
if (TERMINATE_INSTANCE_FEATURE_ACTIVE)
{
LogUtil.Info(logger, "Terminating Instances for AR ID [" + analysisRequest.Id + "]...");
System.Console.WriteLine("\nTerminating Instances for AR ID [" + analysisRequest.Id + "]...");
try
{
//lookup analysis master instances
analysisMasterInstances = cloudComputeService.GetComputeInstances(
new Dictionary <string, List <string> >
{
{ "Name", new List <string> {
"churchill_" + analysisRequest.Id + "_master"
} }
});
//lookup analysis worker instances
analysisWorkerInstances = cloudComputeService.GetComputeInstances(
new Dictionary <string, List <string> >
{
{ "Name", new List <string> {
"churchill_" + analysisRequest.Id + "_worker"
} }
});
//send termination commands to stale AWS instances
try
{
List <string> instancesToTerminate = new List <string>();
//terminate master instances
if (analysisMasterInstances != null && analysisMasterInstances.Sum(r => r.Instances.Count) != 0)
{
instancesToTerminate.AddRange(
analysisMasterInstances.SelectMany(r => r.Instances).Select(i => i.InstanceId).ToList());
}
//terminate worker instances
if (analysisWorkerInstances != null && analysisWorkerInstances.Sum(r => r.Instances.Count) != 0)
{
instancesToTerminate.AddRange(
analysisWorkerInstances.SelectMany(r => r.Instances).Select(i => i.InstanceId).ToList());
}
//submit instance termination request to AWS
if (instancesToTerminate != null && instancesToTerminate.Count != 0)
{
var terminateResult = cloudComputeService.TerminateComputeInstances(instancesToTerminate);
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to Terminate Instances for stale Analysis " + analysisRequest.Id + " : " + e.Message, e);
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to Lookup Instances for stale Analysis " + analysisRequest.Id + " : " + e.Message, e);
}
}
}
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);
}
public override bool ProcessMessage(NewSampleBatch newSampleMessage, object queueMessage)
{
System.Console.WriteLine("***\n ****** Batch Id: " + newSampleMessage.batchId);
System.Console.WriteLine("***\n ****** Sample type: " + newSampleMessage.type);
System.Console.WriteLine("***\n ****** Sample repositoryId: " + newSampleMessage.repositoryId);
SampleResponseService sampleResponseService = new SampleResponseService();
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessage.repositoryId)).FirstOrDefault();
//Find sequencer job
GNSequencerJob sequencerJob = db.GNSequencerJobs.Where(a => a.GNOrganizationId.Equals(Organization.Id) && a.Project.Equals(newSampleMessage.project)).FirstOrDefault();
sequencerJob.Status = "PROCESSING SAMPLES";
GNNewSampleBatch newSampleBatch = new GNNewSampleBatch {
Id = Guid.NewGuid(),
BatchId = newSampleMessage.batchId,
GNSequencerJobId = sequencerJob.Id,
GNSequencerJob = sequencerJob,
Project = newSampleMessage.project,
AutoStartAnalysis = (newSampleMessage.autoStartAnalysis.Equals("true")),
CreateAnalysisPerSample = (newSampleMessage.createAnalysisPerSample.Equals("true")),
Qualifier = newSampleMessage.qualifier,
Type = newSampleMessage.type,
RepositoryId = newSampleMessage.repositoryId,
Gender = newSampleMessage.gender,
ReadType = newSampleMessage.read,
TotalSamples = newSampleMessage.samples.Count(),
TotalSamplesCompleted = 0,
CreateDateTime = DateTime.Now
};
db.GNNewSampleBatches.Add(newSampleBatch);
db.SaveChanges();
bool success = false;
try
{
GNSampleType type = db.GNSampleTypes.Where(a => a.Name.Equals(newSampleMessage.type.ToUpper())).FirstOrDefault();
System.Console.WriteLine("***\n type " + type.Name);
System.Console.WriteLine("***\n Organization " + Organization.Name);
GNTeam newTeam = null;
GNProject newProject = null;
GNAnalysisType analysisType = null;
String AnalysisCode = newSampleMessage.qualifier;
if (newSampleBatch.CreateAnalysisPerSample)
{
/**
* 1. Create a Team
* 2. Create a Project
*/
GNContact contact = db.GNContacts.Find(Organization.GNContactId);
newTeam = new GNTeam
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
Name = "TeamBatch" + newSampleBatch.BatchId.Substring(0, 15),
GNContactId = contact.Id,
Organization = Organization,
OrganizationId = Organization.Id,
TeamLead = contact
};
db.GNTeams.Add(newTeam);
db.SaveChanges();
System.Console.WriteLine("***\n New newTeam Created: " + newTeam.Id);
newProject = new GNProject
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
ProjectLead = contact,
ProjectLeadId = contact.Id.ToString(),
Name = "ProjectBatch-" + newSampleBatch.BatchId.Substring(0, 15),
TeamId = newTeam.Id.ToString(),
StartDate = DateTime.Now,
EndDate = DateTime.Now.AddDays(30),
Description = "Created automatically from the Sample Batch Process"
};
System.Console.WriteLine("***\n New newProject Created: " + newProject.Id);
newTeam.Projects.Add(newProject);
newProject.Teams.Add(newTeam);
db.GNProjects.Add(newProject);
db.SaveChanges();
if (newSampleMessage.qualifier.Equals("TUMOR"))
{
AnalysisCode = "TUMORNORMAL";
}
analysisType = db.GNAnalysisTypes.Where(a => a.Name.Equals(newSampleMessage.type.ToUpper())).FirstOrDefault();
}
foreach (String sampleName in newSampleMessage.samples)
{
String newSampleName = sampleName;
GNSample sampleExist = db.GNSamples.Where(a => a.Name.Equals(sampleName) && a.GNOrganizationId.Equals(Organization.Id)).FirstOrDefault();
bool createNewSample = false;
if (sampleExist != null)
{
if (sampleExist.IsReady)
{
//the sample is ready, let's create a new one with a suffix of (1)
newSampleName = sampleName + " (1)";
createNewSample = true;
}
else
{
//the sample is in the middle of being created, so ignore the message
createNewSample = false;
}
}
else
{
createNewSample = true;
}
try
{
if (createNewSample)
{
GNSample newSample = new GNSample
{
Id = Guid.NewGuid(),
GNOrganizationId = Organization.Id,
Name = newSampleName,
Gender = newSampleMessage.gender,
GNSampleTypeId = type.Id,
GNSampleQualifierCode = newSampleMessage.qualifier,
IsReady = false,
IsPairEnded = (newSampleMessage.read == "paired-end"),
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784")
};
db.GNSamples.Add(newSample);
db.SaveChanges();
System.Console.WriteLine("***\n New Sample Created: " + newSample.Id);
GNNewSampleBatchSamples batchSample = new GNNewSampleBatchSamples {
Id = Guid.NewGuid(),
GNSample = newSample,
CreateDateTime = DateTime.Now,
GNNewSampleBatch = newSampleBatch,
GNNewSampleBatchId = newSampleBatch.Id,
Name = sampleName
};
db.GNNewSampleBatchSamples.Add(batchSample);
db.SaveChanges();
System.Console.WriteLine("***\n New batchSample Created: " + batchSample.Id);
GNNewSampleBatchStatus batchStatus = new GNNewSampleBatchStatus {
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = newSampleBatch,
GNNewSampleBatchId = newSampleBatch.Id,
IsError = false,
PercentComplete = 0,
Status = "STARTING PROCESS",
RepositoryId = newSampleMessage.repositoryId
};
db.GNNewSampleBatchStatus.Add(batchStatus);
db.SaveChanges();
System.Console.WriteLine("***\n New batchStatus Created: " + batchStatus.Id);
if (newSampleBatch.CreateAnalysisPerSample)
{
GNAnalysisRequest newAnalysis = new GNAnalysisRequest {
Id = Guid.NewGuid(),
Project = newProject,
GNProjectId = newProject.Id,
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
AnalysisType = analysisType,
RequestProgress = 0, RequestDateTime = DateTime.Now,
GNAnalysisRequestTypeCode = AnalysisCode,
Description = newSampleName,
GNAnalysisAdaptorCode = "NONE",
AnalysisTypeId = analysisType.Id.ToString(),
AutoStart = newSampleBatch.AutoStartAnalysis,
AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName
};
db.GNAnalysisRequests.Add(newAnalysis);
db.SaveChanges();
System.Console.WriteLine("***\n New newAnalysis Created: " + newAnalysis.Id);
GNAnalysisRequestGNSample newAnalysisSample = new GNAnalysisRequestGNSample {
AffectedIndicator = "N",
TargetIndicator = "N",
GNAnalysisRequest = newAnalysis,
GNSample = newSample,
GNAnalysisRequestId = newAnalysis.Id,
GNSampleId = newSample.Id
};
db.GNAnalysisRequestGNSamples.Add(newAnalysisSample);
} //end of "if(newSampleBatch.CreateAnalysisPerSample)"
System.Console.WriteLine("***\n Sample Name: " + sampleName);
//Notify BCL2FASTQ service
sampleResponseService.NotifyBcl2FastqSystem(newSample, newSampleBatch.RepositoryId);
}
db.SaveChanges();
}
catch (Exception e1)
{
System.Console.WriteLine("***\n Exception: " + e1.Message + e1.InnerException);
}
}
System.Console.WriteLine("***\n EVERYTHING WORKED!");
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_CREATION",
"*****@*****.**",
"Sample Creation",
new Dictionary <string, string>
{
{ "BatchId", newSampleMessage.batchId },
{ "TotalSamples", newSampleBatch.TotalSamples.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "CreateDateTime", DateTime.Now.ToString() }
});
success = true;
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to Create New Sample.", e1);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
/**
* 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;
}
}
/**
* For this batch:
* - Add a status of 90%: Running quality control
* - Check that each sample:
* - Has at least one file
* - If the sample is pair-ended, it has an even number of files
* - If so, change to "is ready"
* If the batch has the "start analysis" in true, start analyses
* Log errors if apply
* Change status to 100% if no errors were found
*/
public void QualityControl(GNNewSampleBatch Batch)
{
bool result = true;
GNNewSampleBatchStatus batchStatus = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = false,
PercentComplete = 90,
Status = "RUNNING QUALITY CONTROL",
Repository = Batch.Repository,
Message = ""
};
db.GNNewSampleBatchStatus.Add(batchStatus);
string errorMessage = "";
foreach (GNNewSampleBatchSamples BatchSample in Batch.GNNewSampleBatchSamples)
{
GNSample sample = BatchSample.GNSample;
if (sample.IsPairEnded && sample.CloudFiles.Count() > 0 && sample.CloudFiles.Count() % 2 == 0)
{
sample.IsReady = true;
}
else if (!sample.IsPairEnded && sample.CloudFiles.Count() > 0 && sample.CloudFiles.Count() % 2 == 1)
{
sample.IsReady = true;
}
else
{
errorMessage += "Sample " + sample.Id.ToString() + "doesn't have the right number of files.\n";
result = false;
}
}
if (result && Batch.AutoStartAnalysis)
{
GNNewSampleBatchStatus batchStatus2 = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = false,
PercentComplete = 95,
Status = "STARTING ANALYSIS",
Repository = Batch.Repository,
Message = ""
};
db.GNNewSampleBatchStatus.Add(batchStatus2);
List <GNAnalysisRequest> analysisRequestsToStart = new List <GNAnalysisRequest>();
foreach (GNNewSampleBatchSamples BatchSample in Batch.GNNewSampleBatchSamples)
{
GNSample sample = BatchSample.GNSample;
GNAnalysisRequest analysis = sample.GNAnalysisRequestGNSamples.FirstOrDefault().GNAnalysisRequest;
if (!analysisRequestsToStart.Contains(analysis))
{
analysisRequestsToStart.Add(analysis);
}
}
foreach (GNAnalysisRequest analysis in analysisRequestsToStart)
{
this.AutostartAnalysis(analysis);
}
GNNewSampleBatchStatus batchStatus3 = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = false,
PercentComplete = 100,
Status = "COMPLETED",
Repository = Batch.Repository,
Message = ""
};
db.GNNewSampleBatchStatus.Add(batchStatus3);
this.NotifyEndOfBatch(Batch);
}
if (!result)
{
GNNewSampleBatchStatus batchStatus4 = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = true,
PercentComplete = 92,
Status = "ERRORS DETECTED",
Repository = Batch.Repository,
Message = ""
};
db.GNNewSampleBatchStatus.Add(batchStatus4);
this.NotifyErrorAtEndOfBatch(Batch, errorMessage);
}
db.SaveChanges();
}
public override bool ProcessMessage(NewSampleBatch newSampleMessage, object queueMessage)
{
System.Console.WriteLine("***\n ****** Batch Id: " + newSampleMessage.batchId);
System.Console.WriteLine("***\n ****** Sample type: " + newSampleMessage.type);
System.Console.WriteLine("***\n ****** Sample repository: " + newSampleMessage.repository);
SampleResponseService sampleResponseService = new SampleResponseService();
List <GNSample> listOfSamples = new List <GNSample>();
List <GNNewSampleBatchSamples> listOfBatchSamples = new List <GNNewSampleBatchSamples>();
List <String> listOfAnalysisNames = new List <String>();
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessage.repository)).FirstOrDefault();
System.Console.WriteLine("***\n Organization " + Organization.Name);
System.Console.WriteLine("***\n Organization Id " + Organization.Id);
System.Console.WriteLine("***\n Project " + newSampleMessage.project);
bool success = false;
try
{
System.Console.WriteLine("***\n Searching sequencerJob ");
//Find sequencer job
GNSequencerJob sequencerJob = db.GNSequencerJobs.Where(a => a.GNOrganizationId.Equals(Organization.Id) && a.Project.Equals(newSampleMessage.project)).FirstOrDefault();
if (sequencerJob == null)
{
throw new Exception("Unable to find Sequencer Job!");
}
sequencerJob.Status = "PROCESSING SAMPLES";
System.Console.WriteLine("***\n Starting. sequencerJob project: " + sequencerJob.Project);
GNProject newProject = sequencerJob.GNProject;
GNTeam newTeam = newProject.Teams.FirstOrDefault();
GNNewSampleBatch newSampleBatch = new GNNewSampleBatch
{
Id = Guid.NewGuid(),
BatchId = newSampleMessage.batchId,
GNSequencerJobId = sequencerJob.Id,
GNSequencerJob = sequencerJob,
Project = newSampleMessage.project,
AutoStartAnalysis = (newSampleMessage.autoStartAnalysis.ToLower().Equals("true")),
CreateAnalysisPerSample = (newSampleMessage.createAnalysisPerSample.ToLower().Equals("true")),
Qualifier = newSampleMessage.qualifier,
Type = newSampleMessage.type,
Repository = newSampleMessage.repository,
ReadType = newSampleMessage.read,
TotalSamples = newSampleMessage.samples.Count(),
TotalSamplesCompleted = 0,
TotalNumberOfFastqFiles = 0,
CreateDateTime = DateTime.Now
};
db.GNNewSampleBatches.Add(newSampleBatch);
GNSampleType type = db.GNSampleTypes.Where(a => a.Name.Equals(newSampleMessage.type.ToUpper())).FirstOrDefault();
System.Console.WriteLine("***\n type " + type.Name);
string datetimeString = DateTime.Now.ToString("MM-dd 0:HH:mm:ss");
GNAnalysisType analysisType = null;
String AnalysisCode = newSampleMessage.qualifier;
if (newSampleBatch.CreateAnalysisPerSample)
{
/**
* 1. Create a Team
* 2. Create a Project
*/
GNContact contact = db.GNContacts.Find(Organization.GNContactId);
if (newSampleMessage.qualifier.Equals("TUMOR"))
{
AnalysisCode = "TUMORNORMAL";
}
analysisType = db.GNAnalysisTypes.Where(a => a.Name.Equals(newSampleMessage.type.ToUpper())).FirstOrDefault();
}
int i = 0;
GNAnalysisRequest newAnalysis = null;
/**
* Loop samples
*/
GNNewSampleBatchStatus batchStatus = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = newSampleBatch,
GNNewSampleBatchId = newSampleBatch.Id,
IsError = false,
PercentComplete = 0,
Status = "STARTING PROCESS",
Repository = newSampleMessage.repository
};
db.GNNewSampleBatchStatus.Add(batchStatus);
System.Console.WriteLine("***\n New batchStatus Created: " + batchStatus.Id);
foreach (SampleBatch sampleBatch in newSampleMessage.samples)
{
String newSampleName = sampleBatch.name;
//tfrege 2016.12.07 do not append family id to sample name anymore
/*
* if(sampleBatch.familyId != "")
* {
* newSampleName = newSampleName + " (" + sampleBatch.familyId + ")";
* System.Console.WriteLine("***\n -------------> newSampleName: " + newSampleName);
* }
*/
GNSample sampleExist = db.GNSamples.Where(a => a.Name.Equals(sampleBatch.name) && a.GNOrganizationId.Equals(Organization.Id)).FirstOrDefault();
bool createNewSample = false;
//Since BCL2FASTQ is not passing gender for now, figure it out based on the family relation
String sampleBatchgender = "U";
switch (sampleBatch.familyRelation)
{
case "F":
case "S":
sampleBatchgender = "M";
break;
case "M":
case "D":
sampleBatchgender = "F";
break;
default:
sampleBatchgender = "F";
break;
}
if (sampleExist != null)
{
if (sampleExist.IsReady)
{
//the sample is ready, let's create a new one with a suffix of (1)
newSampleName = sampleBatch.name + " (1)";
createNewSample = true;
}
else
{
//the sample is in the middle of being created, so ignore the message
createNewSample = false;
//tfrege remove this control just for testing purposes, create new sample always
newSampleName = sampleBatch.name + " (1)"; //remove this after validation is put back in
createNewSample = true;
}
}
else
{
createNewSample = true;
}
try
{
if (createNewSample)
{
GNReplicate replicate = db.GNReplicates.Where(a => a.Name.Equals("NO")).FirstOrDefault();
GNSample newSample = new GNSample
{
Id = Guid.NewGuid(),
GNOrganizationId = Organization.Id,
Name = newSampleName,
Gender = sampleBatchgender,
GNSampleTypeId = type.Id,
GNSampleQualifierCode = newSampleMessage.qualifier,
IsReady = false,
IsPairEnded = (newSampleMessage.read == "paired-end"),
GNReplicateCode = "0",
GNReplicate = replicate,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy
};
db.GNSamples.Add(newSample);
System.Console.WriteLine("***\n New Sample Created: " + newSample.Id);
string analysisName = sampleBatch.name;
if (sampleBatch.familyId != null)
{
analysisName = sampleBatch.familyId;
}
GNNewSampleBatchSamples batchSample = new GNNewSampleBatchSamples {
Id = Guid.NewGuid(),
GNSample = newSample,
CreateDateTime = DateTime.Now,
GNNewSampleBatch = newSampleBatch,
GNNewSampleBatchId = newSampleBatch.Id,
Name = sampleBatch.name,
Affected = sampleBatch.affected,
Proband = sampleBatch.proband,
FamilyId = sampleBatch.familyId,
RelationId = sampleBatch.familyRelation,
Gender = sampleBatchgender,
AnalysisName = analysisName
};
db.GNNewSampleBatchSamples.Add(batchSample);
System.Console.WriteLine("***\n New batchSample Created: " + batchSample.Id);
System.Console.WriteLine("***\n ====>>>>> Adding to listOfAnalysisNames: " + analysisName);
if (!listOfAnalysisNames.Contains(analysisName))
{
listOfAnalysisNames.Add(analysisName);
}
db.SaveChanges();
System.Console.WriteLine("***\n DB CHANGES SAVED.");
System.Console.WriteLine("***\n Sample Name: " + sampleBatch.name);
//Build list to notify the BCL2FASTQ service later
listOfSamples.Add(newSample);
listOfBatchSamples.Add(batchSample);
}
}
catch (Exception e1)
{
System.Console.WriteLine("***\n Exception: " + e1.Message + e1.StackTrace + e1.InnerException);
}
i++;
}
/**
* Update pedigrees, if applies
*/
int maxPedigreeId = db.GNSampleRelationships.Max(a => a.Id);
System.Console.WriteLine("***\n Updating pedigrees for families ");
foreach (GNNewSampleBatchSamples pedigreeSample in listOfBatchSamples.Where(a => a.Gender != "U" && a.RelationId != ""))
{
switch (pedigreeSample.RelationId)
{
case "F":
case "M":
{
GNSampleRelationshipType relationshipType = db.GNSampleRelationshipTypes.Where(a => a.Name.Equals("SON")).FirstOrDefault();
//find sons and daughters
List <GNNewSampleBatchSamples> sons = listOfBatchSamples.Where(a => a.FamilyId.Equals(pedigreeSample.FamilyId) && a.RelationId.Equals("S")).ToList();
foreach (GNNewSampleBatchSamples son in sons)
{
GNSampleRelationship sampleRelationship = new GNSampleRelationship
{
Id = maxPedigreeId++,
GNLeftSample = pedigreeSample.GNSample,
GNLeftSampleId = pedigreeSample.GNSample.Id,
GNRightSample = son.GNSample,
GNRightSampleId = son.GNSample.Id,
GNSampleRelationshipType = relationshipType,
GNSampleRelationshipTypeId = relationshipType.Id,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy
};
db.GNSampleRelationships.Add(sampleRelationship);
System.Console.WriteLine("***\n Added Son " + son.GNSample.Id + " to Parent Sample : " + pedigreeSample.GNSample.Id);
}
relationshipType = db.GNSampleRelationshipTypes.Where(a => a.Name.Equals("DAUGHTER")).FirstOrDefault();
//find sons and daughters
List <GNNewSampleBatchSamples> daughters = listOfBatchSamples.Where(a => a.FamilyId.Equals(pedigreeSample.FamilyId) && a.RelationId.Equals("D")).ToList();
foreach (GNNewSampleBatchSamples daughter in daughters)
{
GNSampleRelationship sampleRelationship = new GNSampleRelationship
{
Id = maxPedigreeId++,
GNLeftSample = pedigreeSample.GNSample,
GNLeftSampleId = pedigreeSample.GNSample.Id,
GNRightSample = daughter.GNSample,
GNRightSampleId = daughter.GNSample.Id,
GNSampleRelationshipType = relationshipType,
GNSampleRelationshipTypeId = relationshipType.Id,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy
};
db.GNSampleRelationships.Add(sampleRelationship);
System.Console.WriteLine("***\n Added Daughter " + daughter.GNSample.Id + " to Parent Sample : " + pedigreeSample.GNSample.Id);
}
} break;
case "S":
case "D":
{
GNSampleRelationshipType relationshipType = db.GNSampleRelationshipTypes.Where(a => a.Name.Equals("FATHER")).FirstOrDefault();
//find sons and daughters
List <GNNewSampleBatchSamples> fathers = listOfBatchSamples.Where(a => a.FamilyId.Equals(pedigreeSample.FamilyId) && a.RelationId.Equals("F")).ToList();
foreach (GNNewSampleBatchSamples dad in fathers)
{
GNSampleRelationship sampleRelationship = new GNSampleRelationship
{
Id = maxPedigreeId++,
GNLeftSample = pedigreeSample.GNSample,
GNLeftSampleId = pedigreeSample.GNSample.Id,
GNRightSample = dad.GNSample,
GNRightSampleId = dad.GNSample.Id,
GNSampleRelationshipType = relationshipType,
GNSampleRelationshipTypeId = relationshipType.Id,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy
};
db.GNSampleRelationships.Add(sampleRelationship);
System.Console.WriteLine("***\n Added Dad " + dad.GNSample.Id + " to Child Sample : " + pedigreeSample.GNSample.Id);
}
relationshipType = db.GNSampleRelationshipTypes.Where(a => a.Name.Equals("MOTHER")).FirstOrDefault();
//find sons and daughters
List <GNNewSampleBatchSamples> mothers = listOfBatchSamples.Where(a => a.FamilyId.Equals(pedigreeSample.FamilyId) && a.RelationId.Equals("M")).ToList();
foreach (GNNewSampleBatchSamples mom in mothers)
{
GNSampleRelationship sampleRelationship = new GNSampleRelationship
{
Id = maxPedigreeId++,
GNLeftSample = pedigreeSample.GNSample,
GNLeftSampleId = pedigreeSample.GNSample.Id,
GNRightSample = mom.GNSample,
GNRightSampleId = mom.GNSample.Id,
GNSampleRelationshipType = relationshipType,
GNSampleRelationshipTypeId = relationshipType.Id,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy
};
db.GNSampleRelationships.Add(sampleRelationship);
System.Console.WriteLine("***\n Added Mom " + mom.GNSample.Id + " to Child Sample : " + pedigreeSample.GNSample.Id);
}
} break;
case "U":
default:
//don't do a thing.
System.Console.WriteLine("***\n Relation is undefined, do not add anything.");
break;
}
}
/******************************************************************************************************/
//SAVE ALL CHANGES (new team, new project, new samples, new analyses, new batch records, new pedigrees)
/******************************************************************************************************/
try
{
db.SaveChanges();
}
catch (Exception eRDS)
{
System.Console.WriteLine("***EXCEPTION DB!!! " + eRDS.Message + " " + eRDS.StackTrace + " " + eRDS.InnerException);
}
try
{
if (newSampleMessage.autoStartAnalysis.ToLower().Equals("true"))
{
System.Console.WriteLine("***\n Elements: " + listOfAnalysisNames.Count());
foreach (String anName in listOfAnalysisNames)
{
List <GNNewSampleBatchSamples> samplesForAnalysis = new List <GNNewSampleBatchSamples>();
newAnalysis = new GNAnalysisRequest
{
Id = Guid.NewGuid(),
Project = newProject,
GNProjectId = newProject.Id,
CreateDateTime = DateTime.Now,
CreatedBy = CreatedBy,
AnalysisType = analysisType,
RequestProgress = 0,
RequestDateTime = DateTime.Now,
GNAnalysisRequestTypeCode = AnalysisCode,
Description = anName,
GNAnalysisAdaptorCode = "NONE",
AnalysisTypeId = analysisType.Id.ToString(),
AutoStart = (newSampleMessage.autoStartAnalysis.ToLower().Equals("true")),
AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName
};
db.GNAnalysisRequests.Add(newAnalysis);
System.Console.WriteLine("***\n ========================\n New newAnalysis Created: " + newAnalysis.Id);
samplesForAnalysis = db.GNNewSampleBatchSamples.Where(a => a.GNNewSampleBatchId.Equals(newSampleBatch.Id) && a.AnalysisName.Equals(anName)).ToList();
foreach (GNNewSampleBatchSamples sample in samplesForAnalysis)
{
GNAnalysisRequestGNSample newAnalysisSample = new GNAnalysisRequestGNSample
{
AffectedIndicator = sample.Affected,
TargetIndicator = sample.Proband,
GNAnalysisRequest = newAnalysis,
GNSample = sample.GNSample,
GNAnalysisRequestId = newAnalysis.Id,
GNSampleId = sample.GNSample.Id
};
db.GNAnalysisRequestGNSamples.Add(newAnalysisSample);
System.Console.WriteLine("***\n Sample Added to New newAnalysis: " + sample.GNSample.Name);
}
}
} //end of "if(newSampleBatch.CreateAnalysisPerSample)"
}
catch (Exception eAnalysis)
{
System.Console.WriteLine("***\n Exception: " + eAnalysis.Message + eAnalysis.StackTrace + eAnalysis.InnerException);
}
db.SaveChanges();
//Notify BCL2FASTQ service
sampleResponseService.NotifyBcl2FastqSystem(listOfBatchSamples);
System.Console.WriteLine("***\n EVERYTHING WORKED!");
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_CREATION",
Organization.OrgMainContact.Email,
"Sample Creation",
new Dictionary <string, string>
{
{ "BatchId", newSampleMessage.batchId },
{ "TotalSamples", newSampleBatch.TotalSamples.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "JobId", sequencerJob.Id.ToString() },
{ "ProjectName", sequencerJob.Project },
{ "CreateDateTime", DateTime.Now.ToString() }
});
success = true;
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to Create New Sample.", e1);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
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);
}
