private static void GetCurrentProject(ActionExecutingContext filterContext, GNEntityModelContainer db)
{
try
{
GNProject currentProject = null;
string projectId = filterContext.HttpContext.Request["projectId"];
if (!string.IsNullOrEmpty(projectId))
{
currentProject = db.GNProjects.Find(Guid.Parse(projectId));
}
if (currentProject != null)
{
filterContext.Controller.ViewBag.CurrentProject = currentProject;
}
else
{
filterContext.Controller.ViewBag.CurrentProject = null;
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to retrieve Current Project!!", 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));
}
public override bool ProcessMessage(Sequencer sequencerMsg, object queueMessage)
{
System.Console.WriteLine("***\n ****** bucket Name: " + sequencerMsg.bucket);
System.Console.WriteLine("***\n ****** project name: " + sequencerMsg.project_name);
bool success = false;
try
{
System.Console.WriteLine("***\n Searching for Org " + sequencerMsg.bucket);
GNOrganization organization = db.GNOrganizations.Where(a => a.Repository.Equals(sequencerMsg.bucket)).FirstOrDefault();
System.Console.WriteLine("***\n ****** organization: " + organization.Name);
if (organization == null)
{
System.Console.WriteLine("***\n NO ORG FOUND!!!!");
return(success);
}
System.Console.WriteLine("***\n organization: " + organization.Id);
if (sequencerMsg.bucket.Equals("ERROR") && sequencerMsg.project_name.Equals("UNDEFINED"))
{
this.NotifyError(sequencerMsg);
return(true);
}
//check if a project is already undergoing for the same Org and same name (repeated message)
int seqJobsRunning = db.GNSequencerJobs.Where(a => a.GNOrganizationId.Equals(organization.Id) && a.Project.Equals(sequencerMsg.project_name.Trim())).Count();
//if none exists, create
if (seqJobsRunning == 0)
{
string datetimeString = DateTime.Now.ToString("MM-dd 0:HH:mm:ss");
/**
* 1. Create a Team
* 2. Create a Project
*/
GNContact contact = db.GNContacts.Find(organization.GNContactId);
GNTeam newTeam = new GNTeam
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
CreatedBy = organization.GNContactId,
Name = "Batch " + datetimeString,
GNContactId = contact.Id,
Organization = organization,
OrganizationId = organization.Id,
TeamLead = contact
};
System.Console.WriteLine("***\n New newTeam Created: " + newTeam.Id);
Guid newProjectId = Guid.NewGuid();
System.Console.WriteLine("*********************************\n Contact for project: " + contact.FullName);
System.Console.WriteLine("*********************************\n Contact for project: " + newProjectId);
GNProject newProject = new GNProject
{
Id = newProjectId,
CreateDateTime = DateTime.Now,
CreatedBy = organization.GNContactId,
ProjectLead = contact,
ProjectLeadId = contact.Id.ToString(),
Name = sequencerMsg.project_name, //name assigned to the project
TeamId = newTeam.Id.ToString(),
StartDate = DateTime.Now,
EndDate = DateTime.Now.AddDays(30),
Description = "Created automatically from the Sample Batch Process"
};
newTeam.Projects.Add(newProject);
newProject.Teams.Add(newTeam);
db.GNTeams.Add(newTeam);
db.GNProjects.Add(newProject);
System.Console.WriteLine("*********************************\n Contact for project: " + newProjectId);
GNSequencerJob sequencerJob = new GNSequencerJob
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
Project = sequencerMsg.project_name,
Status = "STARTED",
GNOrganization = organization,
GNOrganizationId = organization.Id,
GNProject = newProject
};
db.GNSequencerJobs.Add(sequencerJob);
System.Console.WriteLine("***\n New sequencerJob Created: " + sequencerJob.Id);
try
{
db.SaveChanges();
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SEQUENCER_JOB_STARTED",
"*****@*****.**",
"SequencerJob:" + sequencerJob.Id.ToString(),
new Dictionary <string, string>
{
{ "JobId", sequencerJob.Id.ToString() },
{ "ProjectName", sequencerJob.Project },
{ "CreateDateTime", DateTime.Now.ToString() }
});
success = true;
}
catch (Exception eRDS)
{
System.Console.WriteLine("***\n EXCEPCION!!! " + eRDS.Message + eRDS.StackTrace + eRDS.InnerException);
success = false;
}
}
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to process Sequencer Job Message.", e1);
System.Console.WriteLine("***\n EXCEPCION!!! " + e1.Message + e1.StackTrace);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
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);
}
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 GNAnalysisRequest DetailsOnLoad(GNAnalysisRequest analysisRequest)
{
EvalActionPrivileges(analysisRequest);
GNCloudStorageService st = new GNCloudStorageService();
// bool res = ((AnalysisRequestService)entityService).tempPersistStatus(analysisRequest);
auditResult = audit.LogEvent(UserContact, analysisRequest.Id, this.ENTITY, this.Request.UserHostAddress, EVENT_LOAD_DETAILS_UI);
//In case during the creation of result files all where left as type=6, review and update to the corredct types.
try
{
if (analysisRequest.AnalysisResult != null && analysisRequest.AnalysisResult.ResultFiles != null)
{
if (analysisRequest.AnalysisResult.ResultFiles.Where(a => a.GNCloudFileCategoryId == 6).Count() > 0)
{
((AnalysisRequestService)entityService).UpdateFileExtensions(analysisRequest.AnalysisResult);
}
}
}
catch (Exception e)
{
}
//Breadcrumbs Info
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;
ViewBag.DateVCFSentToCartagenia = "NO";
try
{
string stsCartagenia = "CARTAGENIA";
GNAnalysisStatus statusCartagenia = db.GNAnalysisStatus.Where(a => a.GNAnalysisRequestId == analysisRequest.Id && a.Status == stsCartagenia).FirstOrDefault();
if (statusCartagenia != null)
{
ViewBag.DateVCFSentToCartagenia = TimeZoneInfo.ConvertTime((DateTime)statusCartagenia.CreateDateTime, analysisRequest.Project.Teams.FirstOrDefault().Organization.OrgTimeZoneInfo).ToString();
}
}
catch (Exception notFound)
{
ViewBag.DateVCFSentToCartagenia = "NO";
}
GNSettingsTemplate Template = db.GNOrganizations.Where(a => a.Id.Equals(Team.OrganizationId)).FirstOrDefault().GNSettingsTemplate;
ViewBag.TemplateConfigTertiaryFrequency = (Double.Parse(Template.GNSettingsTemplateConfigs.Where(a => a.GNSettingsTemplateField.Id.Equals("TERTIARY_FREQUENCY")).FirstOrDefault().Value) * 100);
ViewBag.TemplateConfigTertiarySplicingTreshold = Template.GNSettingsTemplateConfigs.Where(a => a.GNSettingsTemplateField.Id.Equals("TERTIARY_SPLICING_THRESHOLD")).FirstOrDefault().Value;
//2016.02.04 if the last status was error due to a corrupted file, attach the name of the file to the short status
ViewBag.CorruptFilenameFound = "NA";
if (analysisRequest.CurrentStatusShort.Equals("ERROR"))
{
string lastStatusReported = analysisRequest.AnalysisStatus.LastOrDefault().Message;
if (lastStatusReported.Contains("corrupt file"))
{
string corruptFileName = lastStatusReported.Substring(lastStatusReported.LastIndexOf('/') + 1);
ViewBag.CorruptFilenameFound = analysisRequest.CurrentStatusShort + ": corrupt file found " + corruptFileName;
}
}
if (Request["sampleId"] != null)
{
Guid sampleId = Guid.Parse(Request["sampleId"]);
GNSample Sample = db.GNSamples.Where(a => a.Id.Equals(sampleId)).FirstOrDefault();
ViewBag.CurrentSample = Sample;
}
return(base.DetailsOnLoad(analysisRequest));
}
