/////////////////////////////////////////////////////////////////////////////////
// Register Contact / User
/////////////////////////////////////////////////////////////////////////////////
// GET: Register/Contact
public async Task <ActionResult> Contact(Guid organizationId, Guid contactId)
{
GNOrganization organization = await organizationService.Find(organizationId);
GNContact contact = await contactService.Find(contactId);
if (contact != null && contact.IsInviteAccepted.HasValue && contact.IsInviteAccepted.Value)
{
return(RedirectToAction("ContactComplete", new { id = contact.Id }));
}
RegisterContactViewModel model = new RegisterContactViewModel
{
OrgId = organization.Id,
OrgName = organization.Name,
ContactId = contact.Id,
Email = contact.Email,
FirstName = contact.FirstName,
LastName = contact.LastName,
Title = contact.Title,
Phone = contact.Phone,
Fax = contact.Fax,
Website = contact.Website,
StreetAddress1 = contact.StreetAddress1,
StreetAddress2 = contact.StreetAddress2,
City = contact.City,
State = contact.State,
Zip = contact.Zip,
};
return(View(model));
}
public ActionResult MyOrganization()
{
auditResult = audit.LogEvent(UserContact, UserContact.Id, this.ENTITY, this.Request.UserHostAddress, "VIEW_MY_ORGANIZATION");
var contact = (GNContact)ViewBag.ContactForUser;
GNOrganization organization = db.GNOrganizations.Find(contact.GNOrganizationId);
if (organization == null)
{
return(HttpNotFound());
}
//eval CanInvite
GNContact contactObj = new GNContact
{
GNOrganizationId = UserContact.GNOrganizationId
};
contactObj = contactService.EvalEntitySecurity(UserContact, contactObj);
ViewBag.CanInvite = contactObj.CanCreate;
EvalCanViewContact();
return(View(organization));
}
private async Task <GNOrganization> InsertNewOrganization(RegisterAccountViewModel model)
{
GNOrganization org = null;
try
{
//insert new Org
org = new GNOrganization
{
Name = model.OrgName,
UTCOffsetDescription = model.UTCOffsetDescription,
AWSConfigId = base.db.AWSConfigs.FirstOrDefault().Id,
CreateDateTime = DateTime.Now,
};
org = await organizationService.Insert(org);
}
catch (Exception ex)
{
var ex2 = new Exception("Unable to add Organization.", ex);
LogUtil.Error(logger, ex2.Message, ex2);
throw ex2;
}
return(org);
}
public async Task <ActionResult> AccountComplete(Guid?id)
{
GNOrganization org = await organizationService.Find(id);
ViewBag.userForMainOrgContact = this.identityDB.AspNetUsers.Find(org.OrgMainContact.AspNetUserId);
return(View(org));
}
public void NotifyError(Sequencer sequencerMsg)
{
Guid OrgId = Guid.Parse("82ff6451-dac6-4a88-a967-cdaf5f9a3599");
GNOrganization Organization = db.GNOrganizations.Find(OrgId);
//NOTIFY USER
bool notifyError =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SEQUENCER_JOB_ERROR",
"*****@*****.**",
"SequencerJobError",
new Dictionary <string, string>
{
{ "Message", sequencerMsg.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
public override async Task <ActionResult> Index()
{
EvalCanCreate();
auditResult = audit.LogEvent(UserContact, Guid.Empty, this.ENTITY, this.Request.UserHostAddress, EVENT_LOAD_INDEX_UI);
List <GNContact> contacts = null;
GNTeam team = null;
if (!string.IsNullOrEmpty(Request["teamId"]))
{
team = entityService.db.GNTeams.Find(Guid.Parse(Request["teamId"]));
ViewBag.Team = team;
}
GNOrganization org = null;
if (!string.IsNullOrEmpty(Request["organizationId"]) || team != null)
{
if (team != null)
{
org = team.Organization;
}
else
{
org = entityService.db.GNOrganizations.Find(Guid.Parse(Request["organizationId"]));
}
ViewBag.Organization = org;
contacts = await((ContactService)this.entityService).FindAllByOrg(UserContact, IndexStart(), IndexEnd(), IndexFilters(), org.Id);
}
else
{
contacts = await this.entityService.FindAll(UserContact, IndexStart(), IndexEnd(), IndexFilters());
}
return(View(contacts));
}
private async Task <GNAccount> InsertNewOrgAccount(GNOrganization org, GNContact mainOrgContact,
double maxBalanceAllowed = 0.0, bool validBillingAgreementRequired = true)
{
GNAccount acct = null;
try
{
acct = new GNAccount
{
Id = Guid.NewGuid(),
Organization = org,
GNAccountTypeId = this.db.GNAccountTypes.Where(t => t.Name == "INDUSTRY").Select(t => t.Id).FirstOrDefault(),
AccountOwner = mainOrgContact,
BillingContact = mainOrgContact,
MailingContact = mainOrgContact,
CreateDateTime = DateTime.Now,
CreatedBy = mainOrgContact.Id,
DefaultDiscountAmount = 0.0,
DefaultDiscountType = GNAccount.DiscountType.FLAT.GetCode(),
BillingMode = GNAccount.BillingModeType.INVOICE.GetCode(),
TotalAmountOwed = 0,
TotalAmountPaid = 0,
MaxBalanceAllowed = maxBalanceAllowed,
ValidBillingAgreementRequired = validBillingAgreementRequired
};
acct = this.db.GNAccounts.Add(acct);
int result = await this.db.SaveChangesAsync();
}
catch (Exception ex)
{
var ex2 = new Exception("Unable to add Account for Organization.", ex);
LogUtil.Error(logger, ex2.Message, ex2);
throw ex2;
}
return(acct);
}
private async Task <GNContact> InsertMainOrgContact(RegisterAccountViewModel model, AspNetUser aspNetUser, GNOrganization org)
{
GNContact mainOrgContact = null;
try
{
//find ORG_MANAGER role
AspNetRole aspNetRole = base.identityDB.AspNetRoles.Where(r => r.Name == "ORG_MANAGER").FirstOrDefault();
//insert Main Org Contact with ORG_MANAGER role
mainOrgContact = new GNContact
{
AspNetUserId = aspNetUser.Id,
Email = model.Email,
FirstName = model.FirstName,
LastName = model.LastName,
Title = model.Title,
Phone = model.Phone,
Fax = model.Fax,
Website = model.Website,
StreetAddress1 = model.StreetAddress1,
StreetAddress2 = model.StreetAddress2,
City = model.City,
State = model.State,
Zip = model.Zip,
TermsAcceptDateTime = DateTime.Now,
PrivacyPolicyAcceptDateTime = DateTime.Now,
CreateDateTime = DateTime.Now,
GNOrganizationId = org.Id,
IsSubscribedForNewsletters = model.SignUpForNewsAndProducts
};
mainOrgContact = await contactService.Insert(mainOrgContact);
//Update Org
org.GNContactId = mainOrgContact.Id;
org.CreatedBy = mainOrgContact.Id;
org = await organizationService.Update(org);
if (org != null)
{
mainOrgContact.CreatedBy = mainOrgContact.Id;
mainOrgContact.GNOrganizationId = org.Id;
mainOrgContact.GNContactRoles = new List <GNContactRole>();
mainOrgContact.GNContactRoles.Add(new GNContactRole
{
AspNetRoleId = aspNetRole.Id,
CreatedBy = mainOrgContact.Id,
CreateDateTime = DateTime.Now
});
mainOrgContact = await contactService.Update(org.OrgMainContact);
}
}
catch (Exception ex)
{
var ex2 = new Exception("Unable to add Main Organization Contact.", ex);
LogUtil.Error(logger, ex2.Message, ex2);
throw ex2;
}
return(mainOrgContact);
}
public async Task <ActionResult> AccountSubmit(RegisterAccountViewModel model)
{
if (ModelState.IsValid)
{
GNInviteCode inviteCodeRedemption = null;
try
{
//redeem invite code
inviteCodeRedemption = inviteCodeService.RedeemInviteCode(model.InviteCode);
if (inviteCodeRedemption != null)
{
//Auth or Create User
AspNetUser aspNetUser = await AuthCreateUser(model.Email, model.Password, model.IsExistingUser,
verifyEmail : true, signUpForNews : model.SignUpForNewsAndProducts, organizationId : null);
if (ModelState.IsValid && aspNetUser != null)
{
//Insert New Org
GNOrganization org = await InsertNewOrganization(model);
if (org != null)
{
//Insert Main Org Contact
GNContact mainOrgContact = await InsertMainOrgContact(model, aspNetUser, org);
if (mainOrgContact != null)
{
double maxBalanceAllowed = 0.0;
bool validBillingAgreementRequired = false;
//set free credit allowance based on invite code redemption
if (inviteCodeRedemption.FreeCreditAllowance > 0.0)
{
maxBalanceAllowed = inviteCodeRedemption.FreeCreditAllowance;
}
GNAccount orgAccount =
await InsertNewOrgAccount(org, mainOrgContact, maxBalanceAllowed, validBillingAgreementRequired);
if (inviteCodeRedemption.InviteCode.Equals("GENandGEN2015"))
{
org.GNSettingsTemplate = db.GNSettingsTemplates.Where(a => a.Name == "GN_GENOMICS2015").FirstOrDefault();
db.SaveChanges();
}
if (orgAccount != null)
{
if (model.IsExistingUser)
{
//send notification
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"ORG_ACCOUNT_REGISTRATION_COMPLETE",
mainOrgContact.Email,
"Account:" + mainOrgContact.Id.ToString(),
new Dictionary <string, string>
{
{ "OrganizationName", orgAccount.Organization.Name },
{ "FirstName", mainOrgContact.FirstName },
{ "LastName", mainOrgContact.LastName }
});
}
return(RedirectToAction("AccountComplete", new { id = org.Id }));
}
}
}
}
}
else
{
ModelState.AddModelError("InviteCode", "Unable to redeem Invite Code.");
}
}
catch (Exception ex)
{
LogUtil.Error(logger, "Unable to perform Account Registration", ex);
ModelState.AddModelError("", "Unable to perform Account Registration");
}
if (inviteCodeRedemption != null)
{
inviteCodeService.UnRedeemInviteCode(model.InviteCode);
}
}
return(View(model));
}
// For more information on configuring authentication, please visit http://go.microsoft.com/fwlink/?LinkId=301864
public void ConfigureAuth(IAppBuilder app)
{
// Configure the db context and user manager to use a single instance per request
app.CreatePerOwinContext(GNIdentityDbContext.Create);
app.CreatePerOwinContext <ApplicationUserManager>(ApplicationUserManager.Create);
// JLS: Ensure that, by default, the system will authenticate requests with our configured CookieAuthentication.
app.SetDefaultSignInAsAuthenticationType(DefaultAuthenticationTypes.ApplicationCookie);
//JLS: ***********************************************
app.UseWsFederationAuthentication(
new WsFederationAuthenticationOptions
{
AuthenticationType = "Sanford",
Wtrealm = ConfigurationManager.AppSettings["Sanford:Wtrealm"],
MetadataAddress = ConfigurationManager.AppSettings["Sanford:Metadata"],
Notifications = new WsFederationAuthenticationNotifications
{
AuthenticationFailed = context =>
{
context.HandleResponse();
//JLS: ToDo: Replace this target of this redirect with the appropriate URL for the GenomeNext application.
context.Response.Redirect("Home/Error?message=" + context.Exception.Message);
return(Task.FromResult(-1));
},
//SecurityTokenReceived
SecurityTokenValidated = context =>
{
var userEmail = context.AuthenticationTicket.Identity.FindFirst(ClaimTypes.Email).Value;
var identityDB = new IdentityModelContainer();
var db = new GNEntityModelContainer();
GNContact contact;
AspNetUser user = identityDB.AspNetUsers.Where(a => a.Email.ToLower().Equals(userEmail.ToLower())).FirstOrDefault();
if (user != null)
{
//exists
contact = db.GNContacts.Where(a => a.User.Id.Equals(user.Id) && a.IsInviteAccepted == true).FirstOrDefault();
}
else
{
//create new
String ssoEmail = context.AuthenticationTicket.Identity.FindFirst(ClaimTypes.Email).Value;
GNOrganization organization = db.GNOrganizations.Where(a => a.Name.Contains("Sanford")).FirstOrDefault();
AspNetUser newUser = new AspNetUser
{
Id = Guid.NewGuid().ToString(),
Email = ssoEmail,
IsAdmin = false,
Password = "******",
UserName = ssoEmail,
EmailConfirmed = true
};
identityDB.AspNetUsers.Add(newUser);
contact = new GNContact
{
Id = Guid.NewGuid(),
AspNetUserId = newUser.Id,
CreateDateTime = DateTime.Now,
Email = ssoEmail,
FirstName = context.AuthenticationTicket.Identity.FindFirst(ClaimTypes.GivenName).Value
};
db.GNContacts.Add(contact);
identityDB.SaveChanges();
db.SaveChanges();
}
var applicationUserIdentity = new ClaimsIdentity();
applicationUserIdentity.AddClaim(new Claim(ClaimTypes.Name, contact.FullName, ""));
applicationUserIdentity.AddClaim(new Claim(ClaimTypes.Email, user.Email, ""));
context.OwinContext.Authentication.User.AddIdentity(applicationUserIdentity);
context.Response.Redirect("Home");
return(Task.FromResult(0));
}
}
}
);
//JLS: ***********************************************
// Enable the application to use a cookie to store information for the signed in user
// and to use a cookie to temporarily store information about a user logging in with a third party login provider
// Configure the sign in cookie
app.UseCookieAuthentication(new CookieAuthenticationOptions
{
AuthenticationType = DefaultAuthenticationTypes.ApplicationCookie,
LoginPath = new PathString("/Account/Login"),
ExpireTimeSpan = TimeSpan.FromMinutes(30),
Provider = new CookieAuthenticationProvider
{
OnValidateIdentity = SecurityStampValidator.OnValidateIdentity <ApplicationUserManager, ApplicationUser>(
validateInterval: TimeSpan.FromMinutes(30),
regenerateIdentity: (manager, user) => user.GenerateUserIdentityAsync(manager))
}
});
}
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 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(NewSampleBatchStatus newSampleMessageStatus, object queueMessage)
{
System.Console.WriteLine("***\n newSampleMessageStatus Batch Name: " + newSampleMessageStatus.batchId);
if (newSampleMessageStatus.batchId.Equals("NO_SAMPLE_FOUND"))
{
//processSpecialCases();
}
if (newSampleMessageStatus.status.Equals("QC-COMPLETED"))
{
// ProcessQCMessage(newSampleMessageStatus);
return(true);
}
bool success = false;
try
{
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessageStatus.repositoryId)).FirstOrDefault();
GNNewSampleBatch Batch = db.GNNewSampleBatches.Where(a => a.BatchId.Equals(newSampleMessageStatus.batchId)).FirstOrDefault();
bool isError = false;
if (newSampleMessageStatus.isError.Equals("true"))
{
isError = true;
}
GNNewSampleBatchStatus batchStatus = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = isError,
PercentComplete = newSampleMessageStatus.percentComplete,
Status = newSampleMessageStatus.status,
RepositoryId = newSampleMessageStatus.repositoryId,
FilesBucket = newSampleMessageStatus.filesBucket,
Message = newSampleMessageStatus.message
};
db.GNNewSampleBatchStatus.Add(batchStatus);
db.SaveChanges();
/*
* var tx = db.Database.BeginTransaction();
*
* string insertSQL =
* "INSERT INTO [gn].[GNSampleStatus]" +
* "([Id],[GNSampleId],[SampleName],[Repository],[Message],[PercentComplete],[IsError],[CreatedBy],[CreateDateTime])" +
* "VALUES " +
* "(@Id, @GNSampleId, @SampleName, @Repository, @Message, @PercentComplete, @IsError, @CreatedBy, @CreateDateTime)";
*
* db.Database.ExecuteSqlCommand(
* insertSQL,
* new SqlParameter("@Id", Guid.NewGuid()),
* new SqlParameter("@GNSampleId", sample.Id),
* new SqlParameter("@SampleName", newSampleMessageStatus.name),
* new SqlParameter("@Repository", newSampleMessageStatus.repositoryId),
* new SqlParameter("@Message", newSampleMessageStatus.message),
* new SqlParameter("@PercentComplete", newSampleMessageStatus.percentComplete),
* new SqlParameter("@IsError", isError),
* new SqlParameter("@CreatedBy", Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784")),
* new SqlParameter("@CreateDateTime", DateTime.Now));
*
* LogUtil.Warn(logger, insertSQL);
* tx.Commit();
*/
if (newSampleMessageStatus.filesBucket != null && newSampleMessageStatus.filesBucket != "")
{
System.Console.WriteLine("&&&&& \n Will copy files &&&&&&& ");
try
{
/*
* IQueryable<GNSample> listOfSamples = db.GNSamples.Where(a => a.GNNewSampleBatchSample.GNNewSampleBatchId.Equals(Batch.Id));
*
* GNCloudStorageService st = new GNCloudStorageService();
* string originBucket = newSampleMessageStatus.filesBucket;
* originBucket = "tfrege-test-20140711"; //testing purposes
* Dictionary<String, long> listOfFiles = st.ListingObjects(originBucket);
*
* string s3BucketName = st.FetchAWSS3Bucket().ARN;
*
* /*
* //string volume = newSampleMessageStatus.filesBucket.Substring(newSampleMessageStatus.filesBucket.IndexOf("/")+1, )
* string folderPath1 = newSampleMessageStatus.filesBucket.Replace("http://", "");
* folderPath1 = folderPath1.Replace("https://", "");
* int idxSlash = folderPath1.IndexOf("/");
* int strLen = folderPath1.Length;
*
* //string volume = folderPath1.Substring(0, idxSlash);
* //string folderPath = folderPath1.Substring(idxSlash + 1, strLen - idxSlash - 1);
* GNCloudFileCategory fileCategory = db.GNCloudFileCategories.Where(a => a.Id == 1).FirstOrDefault();
*
*
* string volume = s3BucketName;
*
* foreach (GNSample sample in listOfSamples)
* {
* Guid fileId = Guid.NewGuid();
*
* //Create new folder in S3
* st.PutObjectOnBucket(s3BucketName + "fastq/", sample.Id.ToString(), sample.Id.ToString());
* st.PutObjectOnBucket(s3BucketName + "fastq/", sample.Id.ToString() + "/" + fileId.ToString(), sample.Id.ToString() + "/" + fileId.ToString());
*
* string folderPath = "fastq/" + sample.Id.ToString() + "/" + fileId.ToString();
*
*
* var subList = listOfFiles.Where(a => a.Key.Contains(sample.Name));
* foreach (var file in subList)
* {
* System.Console.WriteLine("&&&&& \n Will copy files &&&&&&& "+file.Key);
*
* string fileURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + folderPath + file.Key;
*
* GNCloudFile newFile = new GNCloudFile
* {
* Id = fileId,
* GNCloudFileCategoryId = fileCategory.Id, //FASTQ
* CloudFileCategory = fileCategory,
* FileName = folderPath + file.Key,
* FileURL = fileURL,
* FolderPath = folderPath,
* Volume = volume,
* Description = file.Key,
* FileSize = file.Value,
* AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName,
* CreateDateTime = DateTime.Now,
* CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
* SampleId = sample.Id.ToString()
* };
* db.GNCloudFiles.Add(newFile);
*
* // st.CopyS3Object(originBucket, fileURL, file.Key);
* }
* db.SaveChanges()
*
* }*/
}
catch (Exception filesUpdateExc)
{
System.Console.WriteLine("***\n Unable to Read the Files from S3: " + newSampleMessageStatus.batchId + "\n" + filesUpdateExc.Message + filesUpdateExc.InnerException + filesUpdateExc.StackTrace);
Exception e2 = new Exception("Unable to Read the Files from S3 for this batch New Sample: ", filesUpdateExc);
LogUtil.Warn(logger, filesUpdateExc.Message, filesUpdateExc);
success = false;
}
success = true;
}
////////////////////////////END OF READING FILES FROM S3 AND UPDATING RDS //////////////
if (isError)
{
Batch.GNSequencerJob.Status = "ERROR";
db.SaveChanges();
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_STATUS_UPDATE_ERROR",
"*****@*****.**",
"Sample Status Update",
new Dictionary <string, string>
{
{ "BatchId", newSampleMessageStatus.batchId },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "ErrorMessage", newSampleMessageStatus.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
if (newSampleMessageStatus.percentComplete == 100 || newSampleMessageStatus.percentComplete.Equals("100"))
{
Batch.GNSequencerJob.Status = "COMPLETED";
db.SaveChanges();
if (Batch.AutoStartAnalysis)
{
//loop through all the samples, look for their analyses, and start them.
List <GNNewSampleBatchSamples> ListOfSamples = Batch.GNNewSampleBatchSamples.ToList();
foreach (GNNewSampleBatchSamples batchSample in ListOfSamples)
{
GNSample sample = batchSample.GNSample;
var result = this.AutostartAnalysis(sample);
}
}
try
{
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_STATUS_UPDATE_COMPLETE",
"*****@*****.**",
"Sample Status Update",
new Dictionary <string, string>
{
{ "BatchId", Batch.Id.ToString() },
{ "TotalSamples", Batch.TotalSamples.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "ErrorMessage", newSampleMessageStatus.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
catch (Exception e2)
{
System.Console.WriteLine("***Message " + e2.Message + e2.StackTrace + " **********************************");
}
}
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to Update Status of New Sample.", e1);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
public override bool ProcessMessage(NewSampleResponse newSampleMessage, object queueMessage)
{
System.Console.WriteLine("***\n ****** Sample Name: " + newSampleMessage.name);
System.Console.WriteLine("***\n ****** Sample type: " + newSampleMessage.type);
System.Console.WriteLine("***\n ****** Sample repositoryId: " + newSampleMessage.repositoryId);
bool success = false;
try
{
GNSampleType type = db.GNSampleTypes.Where(a => a.Name.Equals(newSampleMessage.type.ToUpper())).FirstOrDefault();
System.Console.WriteLine("***\n type " + type.Name);
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessage.repositoryId)).FirstOrDefault();
System.Console.WriteLine("***\n Organization " + Organization.Name);
GNSample sampleExist = db.GNSamples.Where(a => a.Name.Equals(newSampleMessage.name) && 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)
newSampleMessage.name = newSampleMessage.name + " (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 = newSampleMessage.name,
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 Sample Name: " + newSampleMessage.name);
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_CREATION",
"*****@*****.**",
"Sample Creation",
new Dictionary <string, string>
{
{ "SampleName", newSample.Name },
{ "SampleId", newSample.Id.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
}
catch (Exception e1)
{
System.Console.WriteLine("***\n Exception: " + e1.Message + e1.InnerException + e1.StackTrace);
}
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 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(NewSampleStatus newSampleMessageStatus, object queueMessage)
{
System.Console.WriteLine("***\n newSampleMessageStatus Sample Name: " + newSampleMessageStatus.name);
if (newSampleMessageStatus.batchId.Equals("NO_SAMPLE_FOUND"))
{
//processSpecialCases();
}
bool success = false;
try
{
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessageStatus.repositoryId)).FirstOrDefault();
GNSample sample = db.GNSamples.Where(a => a.Name.Equals(newSampleMessageStatus.name.ToUpper()) && a.GNOrganizationId.Equals(Organization.Id)).FirstOrDefault();
bool isError = false;
if (newSampleMessageStatus.isError.Equals("true"))
{
isError = true;
}
var tx = db.Database.BeginTransaction();
string insertSQL =
"INSERT INTO [gn].[GNSampleStatus]" +
"([Id],[GNSampleId],[SampleName],[Repository],[Message],[PercentComplete],[IsError],[CreatedBy],[CreateDateTime])" +
"VALUES " +
"(@Id, @GNSampleId, @SampleName, @Repository, @Message, @PercentComplete, @IsError, @CreatedBy, @CreateDateTime)";
db.Database.ExecuteSqlCommand(
insertSQL,
new SqlParameter("@Id", Guid.NewGuid()),
new SqlParameter("@GNSampleId", sample.Id),
new SqlParameter("@SampleName", newSampleMessageStatus.name),
new SqlParameter("@Repository", newSampleMessageStatus.repositoryId),
new SqlParameter("@Message", newSampleMessageStatus.message),
new SqlParameter("@PercentComplete", newSampleMessageStatus.percentComplete),
new SqlParameter("@IsError", isError),
new SqlParameter("@CreatedBy", Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784")),
new SqlParameter("@CreateDateTime", DateTime.Now));
LogUtil.Warn(logger, insertSQL);
tx.Commit();
success = true;
if (newSampleMessageStatus.filesBucket != null && newSampleMessageStatus.filesBucket != "")
{
//update files in Sample
}
if (isError)
{
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_STATUS_UPDATE_ERROR",
"*****@*****.**",
"Sample Status Update",
new Dictionary <string, string>
{
{ "SampleName", sample.Name },
{ "SampleId", sample.Id.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "ErrorMessage", newSampleMessageStatus.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
if (newSampleMessageStatus.percentComplete == 100 || newSampleMessageStatus.percentComplete.Equals("100"))
{
sample.IsReady = true;
db.SaveChanges();
try
{
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_STATUS_UPDATE_COMPLETE",
"*****@*****.**",
"Sample Status Update",
new Dictionary <string, string>
{
{ "SampleName", sample.Name },
{ "SampleId", sample.Id.ToString() },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "ErrorMessage", newSampleMessageStatus.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
catch (Exception e2)
{
System.Console.WriteLine("***Message " + e2.Message + e2.StackTrace + " **********************************");
}
}
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to Update Status of New Sample.", e1);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
public override bool ProcessMessage(NewSampleBatchStatus newSampleMessageStatus, object queueMessage)
{
System.Console.WriteLine("***\n newSampleMessageStatus Batch Name: " + newSampleMessageStatus.batchId);
if (newSampleMessageStatus.batchId.Equals("NO_SAMPLE_FOUND"))
{
//processSpecialCases();
}
if (newSampleMessageStatus.status.Equals("QC-COMPLETED"))
{
// ProcessQCMessage(newSampleMessageStatus);
return(true);
}
bool success = false;
try
{
GNOrganization Organization = db.GNOrganizations.Where(a => a.Repository.Equals(newSampleMessageStatus.repository)).FirstOrDefault();
GNNewSampleBatch Batch = db.GNNewSampleBatches.Where(a => a.BatchId.Trim().Equals(newSampleMessageStatus.batchId)).FirstOrDefault();
if (Batch == null)
{
throw new Exception("Batch not found!");
}
System.Console.WriteLine("\n --==========================---------> Batch " + Batch.Id);
try
{
Batch.TotalNumberOfFastqFiles = Int32.Parse(newSampleMessageStatus.numberOfFastqFiles);
}
catch (Exception numberNull)
{
Batch.TotalNumberOfFastqFiles = 0;
}
System.Console.WriteLine("\n -----------> Organization " + Organization.Name);
bool isError = false;
if (newSampleMessageStatus.isError.Equals("true"))
{
isError = true;
}
string status = newSampleMessageStatus.status;
if (newSampleMessageStatus.percentComplete > 89)
{
//higher percentages will be dealt by the Portal during the Quality Control step
return(true);
}
//check if the status has been already recorded
int alreadyExists = db.GNNewSampleBatchStatus.Where(a => a.GNNewSampleBatch.BatchId.Equals(newSampleMessageStatus.batchId) && a.PercentComplete == newSampleMessageStatus.percentComplete && a.Status.Equals(status)).Count();
if (alreadyExists == 0)
{
GNNewSampleBatchStatus batchStatus = new GNNewSampleBatchStatus
{
Id = Guid.NewGuid(),
CreateDateTime = DateTime.Now,
GNNewSampleBatch = Batch,
GNNewSampleBatchId = Batch.Id,
IsError = isError,
PercentComplete = newSampleMessageStatus.percentComplete,
Status = status,
Repository = newSampleMessageStatus.repository,
Message = newSampleMessageStatus.message
};
db.GNNewSampleBatchStatus.Add(batchStatus);
db.SaveChanges();
System.Console.WriteLine("\n -----------> Added status " + newSampleMessageStatus.status + " " + newSampleMessageStatus.percentComplete + "%");
if (isError)
{
Batch.GNSequencerJob.Status = "ERROR";
db.SaveChanges();
//NOTIFY USER
bool notifySuccess =
new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
"SAMPLE_STATUS_UPDATE_ERROR",
Organization.OrgMainContact.Email,
"Sample Status Update",
new Dictionary <string, string>
{
{ "BatchId", newSampleMessageStatus.batchId },
{ "CreatorName", Organization.OrgMainContact.FullName },
{ "ErrorMessage", newSampleMessageStatus.message },
{ "CreateDateTime", DateTime.Now.ToString() }
});
}
/*
* if (newSampleMessageStatus.percentComplete == 100 || newSampleMessageStatus.percentComplete.Equals("100"))
* {
* Batch.GNSequencerJob.Status = "COMPLETED";
*
*
* //loop through all the samples, look for their analyses, and start them.
* foreach (GNNewSampleBatchSamples sampleBatch in Batch.GNNewSampleBatchSamples)
* {
* sampleBatch.GNSample.IsReady = true;
* }
*
* db.SaveChanges();
*
*
* if (Batch.AutoStartAnalysis)
* {
* //loop through all the samples, look for their analyses, and start them.
* List<GNNewSampleBatchSamples> ListOfSamples = Batch.GNNewSampleBatchSamples.ToList();
*
* foreach (GNNewSampleBatchSamples batchSample in ListOfSamples)
* {
* GNSample sample = batchSample.GNSample;
* var result = this.AutostartAnalysis(sample);
* }
* }
*
* try
* {
* String notifyCreateAnalysis = "";
* if (Batch.CreateAnalysisPerSample)
* {
* notifyCreateAnalysis = "Each sample had one analysis created automatically.";
* }
*
* String notifyAutostartAnalysis = "";
* if (Batch.AutoStartAnalysis)
* {
* notifyAutostartAnalysis = "Each analysis create was autostarted as soon as the samples were completed. New notifications will be sent to your inbox -with links to each analysis- as these move along.";
* }
*
* //NOTIFY USER
* bool notifySuccess =
* new GenomeNext.App.NotificationCloudMessageService().NotifyGNContact(
* "SAMPLE_STATUS_UPDATE_COMPLETE",
* "*****@*****.**", //Organization.OrgMainContact.Email,
* "Sample Status Update",
* new Dictionary<string, string>
* {
* {"ProjectName", Batch.GNSequencerJob.Project},
* {"TotalSamples", Batch.TotalSamples.ToString()},
* {"CreateAnalysisPerSample", notifyCreateAnalysis},
* {"AutoStartAnalysis", notifyAutostartAnalysis},
* {"ErrorMessage", newSampleMessageStatus.message},
* {"CreateDateTime",DateTime.Now.ToString()}
* });
* }
* catch (Exception e2)
* {
* System.Console.WriteLine("***Message " + e2.Message + e2.StackTrace + " **********************************");
*
* }
*
* }
*/
}
success = true;
}
catch (Exception e1)
{
Exception e2 = new Exception("Unable to Update Status of New Sample.", e1);
System.Console.WriteLine("***\n Exception: " + e1.Message + e1.StackTrace + e1.InnerException);
LogUtil.Warn(logger, e2.Message, e2);
success = false;
}
return(success);
}
