public ProjectService(GNEntityModelContainer db, IdentityModelContainer identityDB)
: base(db)
{
base.db = db;
this.aspNetRoleService = new AspNetRoleService(identityDB);
this.teamService = new TeamService(db, identityDB);
}
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);
}
}
private static void GetCurrentSample(ActionExecutingContext filterContext, GNEntityModelContainer db)
{
try
{
GNSample currentSample = null;
string sampleId = filterContext.HttpContext.Request["sampleId"];
if (string.IsNullOrEmpty(sampleId))
{
sampleId = filterContext.HttpContext.Request["GNLeftSampleId"];
}
if (!string.IsNullOrEmpty(sampleId))
{
currentSample = db.GNSamples.Find(Guid.Parse(sampleId));
}
if (currentSample != null)
{
filterContext.Controller.ViewBag.CurrentSample = currentSample;
}
else
{
filterContext.Controller.ViewBag.CurrentSample = null;
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to retrieve Current Sample!!", e);
}
}
public CloudFileService(GNEntityModelContainer db, IdentityModelContainer identityDB)
: base(db)
{
base.db = db;
this.aspNetRoleService = new AspNetRoleService(identityDB);
this.transactionService = new TransactionService(db);
}
public TeamService(GNEntityModelContainer db, IdentityModelContainer identityDB)
{
base.db = db;
this.aspNetRoleService = new AspNetRoleService(identityDB);
this.aspNetUserRoleService = new AspNetUserRoleService(identityDB);
}
public ActiveDirectoryService(GNEntityModelContainer db, IdentityModelContainer identityDB)
{
base.db = db;
this.aspNetRoleService = new AspNetRoleService(identityDB);
this.aspNetUserRolesService = new AspNetUserRoleService(identityDB);
}
public SampleService(GNEntityModelContainer db, IdentityModelContainer identityDB)
: base(db)
{
base.db = db;
this.aspNetRoleService = new AspNetRoleService(identityDB);
this.teamService = new TeamService(db, identityDB);
this.cloudFileService = new CloudFileService(db, identityDB);
}
public AWSComputeEnvironmentService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
AWSConfig awsConfig = db.AWSConfigs.FirstOrDefault();
cloudComputeService = new GNCloudComputeService(awsConfig.Id);
analysisRequestService = new AnalysisRequestService(db, new Data.IdentityModel.IdentityModelContainer());
}
private async Task <int> CreateNewInvoices()
{
int result = 1;
if (DateTime.Now.Day == DAY_TO_CREATE_INVOICES)
{
LogUtil.Info(logger, "CreateNewInvoices()...");
System.Console.WriteLine("\nCreateNewInvoices()...");
var db = new GNEntityModelContainer();
InvoiceService invoiceService = new InvoiceService(db);
InvoiceDetailService invoiceDetailService = new InvoiceDetailService(db);
TransactionService transactionService = new TransactionService(db);
AccountService orgAccountService = new AccountService(db);
foreach (var orgAccount in await orgAccountService.FindAll())
{
try
{
LogUtil.Info(logger, "Account = " + orgAccount.Organization.Name);
System.Console.WriteLine("\nAccount = " + orgAccount.Organization.Name);
//get user contact
GNContact userContact = orgAccount.AccountOwner;
if (userContact == null)
{
userContact = db.GNContacts.Where(c => c.GNOrganizationId == orgAccount.Organization.Id).FirstOrDefault();
}
if (userContact != null)
{
string thisCycle = String.Format("{0:yyyyMM}", DateTime.Now);
GNInvoice newInvoiceMonth = invoiceService.GetInvoiceForDateTime(userContact, thisCycle);
if (newInvoiceMonth == null)
{
newInvoiceMonth = await invoiceService.CreateInvoiceForCurrentMonth(userContact, orgAccount);
}
System.Console.WriteLine("\nInvoice for Cycle " + thisCycle + " for Organization " + orgAccount.Organization.Name + " is " + newInvoiceMonth.Id);
LogUtil.Info(logger, "Invoice for Cycle " + thisCycle + " for Organization " + orgAccount.Organization.Name + " is " + newInvoiceMonth.Id);
}
}
catch (Exception ex)
{
result = 0;
LogUtil.Warn(logger, ex.Message, ex);
System.Console.WriteLine(ex.Message);
}
}
}
return(result);
}
private void GetNavBarInfo(ActionExecutingContext filterContext)
{
if (filterContext != null && filterContext.Controller != null && filterContext.Controller.GetType().GetProperties().Count(p => p.Name == "db") != 0)
{
GNEntityModelContainer db = (GNEntityModelContainer)filterContext.Controller.GetType().GetProperty("db").GetValue(filterContext.Controller);
GetCurrentTeam(filterContext, db);
GetCurrentProject(filterContext, db);
GetCurrentAnalysisRequest(filterContext, db);
GetCurrentSample(filterContext, db);
GetRemainingBudget(filterContext, db);
}
}
public AuditService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
AWSConfig AWSConfigEntity = db.AWSConfigs.FirstOrDefault();
Amazon.RegionEndpoint regionEndpoint =
Amazon.RegionEndpoint.GetBySystemName(AWSConfigEntity.AWSRegionSystemName);
dynamoClient = new AmazonDynamoDBClient(
AWSConfigEntity.AWSAccessKeyId,
AWSConfigEntity.AWSSecretAccessKey,
regionEndpoint);
}
/*
* private async Task<double> GetRemainingBudget(ActionExecutingContext filterContext, GNEntityModelContainer db)
* {
* GNContact userContact = (GNContact)filterContext.Controller.ViewBag.ContactForUser;
*
* if (userContact != null
* && (userContact.IsInRole("GN_ADMIN") || userContact.IsInRole("ORG_MANAGER")))
* {
* var myAccount = db.GNAccounts
* .Where(a => a.Organization.Id == userContact.GNOrganizationId)
* .FirstOrDefault();
*
* if (myAccount != null)
* {
* bool result = await (new InvoiceService(db)).fetchCurrentInvoice(userContact);
*
* filterContext.Controller.ViewBag.MyRemainingBudget =// myAccount.AvailableCredits;
* (new AccountService(db)).GetRemainingBudget(userContact, myAccount);
* }
* }
* return filterContext.Controller.ViewBag.MyRemainingBudget;
* }
*/
private static void GetRemainingBudget(ActionExecutingContext filterContext, GNEntityModelContainer db)
{
GNContact userContact = (GNContact)filterContext.Controller.ViewBag.ContactForUser;
if (userContact != null &&
(userContact.IsInRole("GN_ADMIN") || userContact.IsInRole("ORG_MANAGER")))
{
var myAccount = db.GNAccounts
.Where(a => a.Organization.Id == userContact.GNOrganizationId)
.FirstOrDefault();
if (myAccount != null)
{
filterContext.Controller.ViewBag.MyRemainingBudget =// myAccount.AvailableCredits;
(new AccountService(db)).GetRemainingBudget(userContact, myAccount);
}
}
}
private void InitServices()
{
LogUtil.LogMethod(logger, MethodBase.GetCurrentMethod());
//get mark analysis in error feature setting
bool.TryParse(
System.Configuration.ConfigurationManager.AppSettings["MarkAnalysisInErrorFeatureActive"],
out MARK_ANALYSIS_IN_ERROR_FEATURE_ACTIVE);
//get restart feature setting
bool.TryParse(
System.Configuration.ConfigurationManager.AppSettings["TerminateInstanceFeatureActive"],
out TERMINATE_INSTANCE_FEATURE_ACTIVE);
//get restart feature setting
bool.TryParse(
System.Configuration.ConfigurationManager.AppSettings["RestartAnalysisFeatureActive"],
out RESTART_ANALYSIS_FEATURE_ACTIVE);
//get force restart feature setting
bool.TryParse(
System.Configuration.ConfigurationManager.AppSettings["ForceRestartAnalysis"],
out FORCE_RESTART_ANALYSIS);
if (cloudComputeService == null)
{
LogUtil.Info(logger, GetType().Name + ".InitServices()...");
System.Console.WriteLine("\n" + GetType().Name + ".InitServices()...");
try
{
AWSConfig awsConfig = new GNEntityModelContainer().AWSConfigs.FirstOrDefault();
cloudComputeService = new GNCloudComputeService(awsConfig.Id);
}
catch (Exception ex)
{
LogUtil.Warn(logger, ex.Message, ex);
System.Console.WriteLine(ex.Message);
}
}
}
// 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 IGNCloudMessageService <BamViewer> GetService()
{
AWSConfig awsConfig = new GNEntityModelContainer().AWSConfigs.FirstOrDefault();
return(new AnalysisBamViewerService(awsConfig.Id, AnalysisBamViewerService.QUEUE_NAME));
}
public ReplicateService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public override IGNCloudMessageService <NotificationMessage> GetService()
{
AWSConfig awsConfig = new GNEntityModelContainer().AWSConfigs.FirstOrDefault();
return(new NotificationCloudMessageService(awsConfig.Id, NotificationCloudMessageService.QUEUE_NAME));
}
public NotificationTopicSubscriberService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public NotificationSuppressionListsService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public NotificationTopicAddresseeService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public InviteCodeService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public SampleQualifierGroupService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
private async Task <int> ProcessStorageCarryOverFees()
{
int result = 1;
if (DateTime.Now.Day == DAY_TO_PROCESS_STORAGE_CARRYOVER_FEES)
{
LogUtil.Info(logger, "ProcessStorageCarryOverFees()...");
System.Console.WriteLine("\nProcessStorageCarryOverFees()...");
var db = new GNEntityModelContainer();
InvoiceService invoiceService = new InvoiceService(db);
InvoiceDetailService invoiceDetailService = new InvoiceDetailService(db);
TransactionService transactionService = new TransactionService(db);
AccountService orgAccountService = new AccountService(db);
foreach (var orgAccount in await orgAccountService.FindAll())
{
try
{
LogUtil.Info(logger, "Account = " + orgAccount.Organization.Name);
System.Console.WriteLine("\nAccount = " + orgAccount.Organization.Name);
//get user contact
GNContact userContact = orgAccount.AccountOwner;
if (userContact == null)
{
userContact = db.GNContacts.Where(c => c.GNOrganizationId == orgAccount.Organization.Id).FirstOrDefault();
}
if (userContact != null)
{
//get last month invoice
GNInvoice lastMonthInvoice = invoiceService.GetInvoiceForLastMonth(userContact);
if (lastMonthInvoice != null)
{
string txnKey = "STORAGE_S3_CARRYOVER";
//get invoice to update
GNInvoice invoiceToUpdate = null;
if (lastMonthInvoice.Status != GNInvoice.InvoiceStatus.PAID.ToString() &&
lastMonthInvoice.Status != GNInvoice.InvoiceStatus.VOID.ToString())
{
invoiceToUpdate = lastMonthInvoice;
}
else
{
invoiceToUpdate = await invoiceService.GetInvoiceForCurrentMonth(orgAccount.AccountOwner);
}
if (invoiceToUpdate != null)
{
//get storage carryover detail
GNInvoiceDetail storageCarryOverInvoiceDetail =
db.GNInvoiceDetails
.Where(invd => (invd.GNInvoiceId == invoiceToUpdate.Id && invd.Description == txnKey))
.FirstOrDefault();
//add invoice detail, if missing
if (storageCarryOverInvoiceDetail == null)
{
storageCarryOverInvoiceDetail =
db.GNInvoiceDetails.Add(new GNInvoiceDetail
{
Id = Guid.NewGuid(),
Description = txnKey,
GNInvoiceId = invoiceToUpdate.Id,
Quantity = 0.0,
SubTotal = 0.0,
DiscountAmount = orgAccount.DefaultDiscountAmount,
DiscountType = orgAccount.DefaultDiscountType,
Total = 0.0,
UnitCost = 0.0,
UnitPrice = 0.0,
CreateDateTime = DateTime.Now,
CreatedBy = orgAccount.AccountOwner.Id
});
await db.SaveChangesAsync();
storageCarryOverInvoiceDetail = db.GNInvoiceDetails.Find(storageCarryOverInvoiceDetail.Id);
}
if (storageCarryOverInvoiceDetail != null)
{
//get txn count
int txnCount =
db.GNTransactions.Count(t =>
(t.GNInvoiceDetailId == storageCarryOverInvoiceDetail.Id &&
t.TransactionType.Name == txnKey));
if (txnCount == 0)
{
//get storage balance for month
//all uploads minus all downloads up until end of last month
var storageUsed = orgAccountService.CalcStorageUsed(orgAccount.Id, lastMonthInvoice.InvoiceEndDate.AddDays(1));
//get storage carryover product
GNProduct storageCarryOverProduct = db.GNProducts.Where(p => p.Name == txnKey).FirstOrDefault();
//calc storage carryover cost
var totalCarryOverCost = storageUsed * storageCarryOverProduct.Price;
//add storage cost transaction
string txnTypeKey = txnKey;
string description = storageUsed + "GB";
double valueUsed = storageUsed;
string valueUnits = "GB";
int updateResult = 0;
GNTransaction txn =
await transactionService.CreateTransaction(
userContact, txnTypeKey, description, valueUsed, valueUnits,
targetInvoice : invoiceToUpdate);
if (txn != null)
{
updateResult = 1;
}
//update invoice totals
//int updateResult = await invoiceDetailService.UpdateInvoiceDetailTotals(
// invDetailToUpdate.Id, invDetailToUpdate.GNInvoiceId, invDetailToUpdate.Invoice.GNAccountId);
LogUtil.Info(logger, "Update result = " + updateResult);
System.Console.WriteLine("\nUpdate result = " + updateResult);
}
}
}
}
}
}
catch (Exception ex)
{
result = 0;
LogUtil.Warn(logger, ex.Message, ex);
System.Console.WriteLine(ex.Message);
}
}
}
return(result);
}
private void GetContactForUser(ActionExecutingContext filterContext)
{
try
{
if (filterContext != null && filterContext.Controller != null &&
filterContext.Controller.GetType().GetProperties().Count(p => p.Name == "identityDB") != 0 &&
filterContext.Controller.GetType().GetProperties().Count(p => p.Name == "db") != 0)
{
IdentityModelContainer identityDB = (IdentityModelContainer)filterContext.Controller.GetType().GetProperty("identityDB").GetValue(filterContext.Controller);
GNEntityModelContainer db = (GNEntityModelContainer)filterContext.Controller.GetType().GetProperty("db").GetValue(filterContext.Controller);
var requestUser = filterContext.HttpContext.User;
GNContact contact = null;
if (requestUser != null && requestUser.Identity != null && requestUser.Identity.IsAuthenticated)
{
var user = identityDB.AspNetUsers.Where(u => u.UserName == requestUser.Identity.Name).FirstOrDefault();
if (user != null)
{
Guid defaultOrganizationIdGuid = Guid.Empty;
if (!string.IsNullOrEmpty(user.DefaultOrganizationId))
{
defaultOrganizationIdGuid = Guid.Parse(user.DefaultOrganizationId);
contact = db.GNContacts
.Where(c => (c.AspNetUserId == user.Id && c.GNOrganizationId == defaultOrganizationIdGuid))
.FirstOrDefault();
}
else
{
contact = db.GNContacts
.Where(c => (c.AspNetUserId == user.Id))
.FirstOrDefault();
if (contact != null)
{
user.DefaultOrganizationId = contact.GNOrganizationId.ToString();
identityDB.Entry(user).State = System.Data.Entity.EntityState.Modified;
user.Password = "******";
user.PasswordConfirm = ".";
identityDB.SaveChanges();
}
}
if (contact != null && user != null)
{
contact.User = user;
}
if (contact != null && contact.GNContactRoles != null)
{
foreach (var contactRole in contact.GNContactRoles)
{
contactRole.AspNetRole = identityDB.AspNetRoles.Find(contactRole.AspNetRoleId);
}
}
}
}
if (contact != null)
{
//set contact
filterContext.Controller.ViewBag.ContactForUser = contact;
//set organizations for user contact
filterContext.Controller.ViewBag.OrganizationsForUser =
db.GNContacts
.Where(c => c.AspNetUserId == contact.AspNetUserId)
.Select(c => c.GNOrganization)
.Where(o => o.Id != contact.GNOrganizationId)
.ToList();
//get org settings template for user
var orgConfigSettingsTemplate =
db.GNSettingsTemplates
.Include(t => t.GNSettingsTemplateConfigs)
.Where(t => t.GNOrganizations.Any(o => o.Id == contact.GNOrganizationId))
.FirstOrDefault();
if (orgConfigSettingsTemplate != null &&
orgConfigSettingsTemplate.GNSettingsTemplateConfigs != null &&
orgConfigSettingsTemplate.GNSettingsTemplateConfigs.Count != 0)
{
filterContext.Controller.ViewBag.OrgConfigSettings =
orgConfigSettingsTemplate.GNSettingsTemplateConfigs.ToList();
}
}
else
{
filterContext.Controller.ViewBag.ContactForUser = null;
}
}
}
catch (Exception e)
{
LogUtil.Error(logger, "Unable to Get Contact User!!", e);
}
}
public SampleTypeService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public GeneService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public SampleRelationshipService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public SequencerJobService(GNEntityModelContainer db)
: base(db)
{
base.db = db;
}
public override IGNCloudMessageService <StartVcfStatsReport> GetService()
{
AWSConfig awsConfig = new GNEntityModelContainer().AWSConfigs.FirstOrDefault();
return(new StartQcReportService(awsConfig.Id, StartQcReportService.QUEUE_NAME));
}
public override IGNCloudMessageService <NewSampleBatch> GetService()
{
AWSConfig awsConfig = new GNEntityModelContainer().AWSConfigs.FirstOrDefault();
return(new SampleBatchRequestService(awsConfig.Id, SampleBatchRequestService.QUEUE_NAME));
}