protected override ValidationResult IsValid(object value, ValidationContext validationContext)
{
using (GenomeAssemblyDbContext context = new GenomeAssemblyDbContext())
{
// Grab all the dawgtags.
var userList = context.Users
.Select(u => new { DawgTag = u.DawgTag }).ToList();
// Compare the dawgtags against the entered dawgtag.
foreach (var u in userList)
{
if (u.DawgTag == Convert.ToInt32(value))
{
return(new ValidationResult("That DawgTag is already associated with a user."));
}
}
return(ValidationResult.Success);
}
}
public ActionResult ViewJobs()
{
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
var jobList = from jobs in db.GenomeModels
where jobs.CreatedBy.Equals(User.Identity.Name)
select jobs;
if (jobList.Count() > 0)
{
return(View(jobList.ToList()));
}
else
{
ViewBag.ShowJobList = false;
return(View());
}
}
}
protected override ValidationResult IsValid(object value, ValidationContext validationContext)
{
// First check if the email address is a valid email address.
EmailAddressAttribute emailFormat = new EmailAddressAttribute();
if (emailFormat.IsValid(value))
{
// Check if the email has @siu.edu at the end of the email.
if (Convert.ToString(value).Split('@')[1].Equals("siu.edu"))
{
// Check that the email is currently not in the database.
using (GenomeAssemblyDbContext context = new GenomeAssemblyDbContext())
{
// Grab all the emails.
var userList = context.Users
.Select(u => new { Email = u.Email }).ToList();
// Compare the emails against the entered email.
foreach (var u in userList)
{
if (u.Email.Equals(value))
{
return(new ValidationResult("That email is already associated with a user."));
}
}
return(ValidationResult.Success);
}
}
else
{
return(new ValidationResult("The email address must be a valid SIU email address ending with @siu.edu."));
}
}
else
{
return(new ValidationResult(ErrorMessage));
}
}
public ActionResult Create()
{
// TODO: Need policy-based authorization workaround for this...aka open up the parameter in the account model
// and extending the authorize attribute to include it as a parameter to check all in one sweep. If time permits...
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
string username = HttpContext.User.Identity.GetUserName();
var temp = from u in db.Users
where u.UserName.Equals(username)
select u.ClusterAccountVerified;
// This should only ever be iterated through once.
foreach (var acctStat in temp)
{
if (!acctStat)
{
return(RedirectToAction("CreateJobErrorCluster", "Error"));
}
}
return(View(new GenomeModel()));
}
}
public ActionResult UnverifiedUser()
{
// While this shouldn't necessarily need to be run, there are instances where
// this is necessary to make sure we don't show this page to anything but an unverified user.
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
string username = HttpContext.User.Identity.GetUserName();
var temp = from u in db.Users
where u.UserName.Equals(username)
select u.Roles;
// This should only ever be iterated through once.
foreach (var uRole in temp)
{
if (!uRole.Equals(Helpers.CustomRoles.Unverified))
{
return(RedirectToAction("Index", "Home"));
}
}
}
return(View());
}
/// <summary>
/// Updates the status of a single job. But it does not perform the upload if that needs to happen.
/// </summary>
/// <param name="genomeModel">The model of the particular job.</param>
protected internal static void UpdateStatus(GenomeModel genomeModel)
{
using (var client = new SshClient(CreatePrivateKeyConnectionInfo()))
{
try
{
client.Connect();
/// TODO: Modify the code to skip entire sections if they have already been completed. This will be based off the CURRENT STEP stored in the model data.
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
bool continueUpdate = true; // Determines whether we will continue checking the job status.
bool DEBUG_MODE = false; // Debug mode to skip some assembler steps.
bool outOfRange = false; // If the overall step is out of bounds, then we set this to true to attempt a correction.
ErrorHandling.error = ""; // Reset the errror flag.
while (continueUpdate && ErrorHandling.NoError())
{
// Depending on the current step, this switch will determine if the state of the job needs to change.
switch (genomeModel.OverallCurrentStep)
{
// Queued step
case 1:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (LinuxCommands.IsProcessRunning(client, "conversionScript.sh"))
{
genomeModel.NextStep();
}
// If a conversion was never run or if we missed it, then check if the job has already started.
else if (LinuxCommands.JobRunningAlt(client, genomeModel.SSHUser))
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Data conversion step
case 2:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (LinuxCommands.DirectoryHasFiles(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed)))
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Running assemblers step
case 3:
{
if (DEBUG_MODE)
{
genomeModel.NextStep();
break;
}
if (genomeModel.UseMasurca)
{
CheckMasurcaStep(client, genomeModel);
}
if (genomeModel.UseSGA)
{
}
if (genomeModel.UseWGS)
{
}
if (genomeModel.IsAssemblyFinished())
{
genomeModel.NextStep();
}
else
{
continueUpdate = false;
}
break;
}
// Data analysis step
case 4:
{
// Until data analysis is implemented, we skip the step.
genomeModel.NextStep();
break;
//if (LinuxCommands.IsProcessRunning(client, "dataAnalysis.sh"))
// continueUpdate = false;
//else
//{
// // Has it finished?
// if (LinuxCommands.FileExists(client, Accessors.GetJobOutputPath(genomeModel.Seed) + "dataAnalysisResult"))
// genomeModel.NextStep();
// else
// LinuxCommands.RunDataAnalysis(client);
//}
//break;
}
// TODO: Create a more robust method in checking for a completed upload. Maybe connect to the FTP and compare file sizes and see if they are close.
// Uploading Data step
case 5:
{
//if (LinuxCommands.IsJobUploading(client, Accessors.USER_ROOT_JOB_DIRECTORY, Accessors.GetCompressedDataPath(genomeModel.Seed)))
// continueUpdate = false;
//else if (LinuxCommands.FileExists(client, Accessors.GetCompressedDataPath(genomeModel.Seed)))
// genomeModel.NextStep();
//else
//{
LinuxCommands.UploadJobData(client, Accessors.USER_ROOT_JOB_DIRECTORY, Accessors.GetCompressedDataPath(genomeModel.Seed)
, Accessors.GetRelativeJobDirectory(genomeModel.Seed), Accessors.GetRemoteDownloadLocation(genomeModel.Seed), true, "yr");
continueUpdate = false;
//}
break;
}
// Completed step
case 6:
{
continueUpdate = false;
break;
}
default:
{
// If we have attempted a correction and failed, throw in the towel.
if (outOfRange)
{
throw new IndexOutOfRangeException("The current step of the program is out of bounds after an attempted correction. The current step: "
+ genomeModel.OverallCurrentStep);
}
else
{
outOfRange = true;
// Reset the state to default and have it run through the update method again.
genomeModel.OverallCurrentStep = 1;
genomeModel.OverallStatus = StepDescriptions.GetOverallStepList()[genomeModel.OverallCurrentStep].ToString();
}
break;
}
}
}
}
}
// SSH Connection couldn't be established.
catch (SocketException e)
{
ErrorHandling.error = "The SSH connection couldn't be established. " + e.Message;
}
// The SSH connection was dropped.
catch (SshConnectionException e)
{
ErrorHandling.error = "The connection was terminated unexpectedly. " + e.Message;
}
}
}
//
// GET: /Manage/Index
public async Task <ActionResult> Index(ManageMessageId?message)
{
ViewBag.StatusMessage =
message == ManageMessageId.ChangePasswordSuccess ? "Your password has been changed."
: message == ManageMessageId.SetPasswordSuccess ? "Your password has been set."
: message == ManageMessageId.SetTwoFactorSuccess ? "Your two-factor authentication provider has been set."
: message == ManageMessageId.Error ? "An error has occurred."
: message == ManageMessageId.AddPhoneSuccess ? "Your phone number was added."
: message == ManageMessageId.RemovePhoneSuccess ? "Your phone number was removed."
: "";
var userId = User.Identity.GetUserId();
/// I really need to extend the Identity class to add a get for the verifiedclusteraccount rather than this. BUt it will do for now.
using (GenomeAssemblyDbContext db = new GenomeAssemblyDbContext())
{
string username = HttpContext.User.Identity.GetUserName();
bool verifiedClusterAccount = false;
var usernameLookup = from u in db.Users
where u.UserName.Equals(username)
select u;
var dawgTagLookup = from u in db.Users
where u.UserName.Equals(username)
select u.DawgTag;
int dawgTag = 0;
foreach (var user in dawgTagLookup)
{
dawgTag = user;
}
// This should only ever be iterated through once.
foreach (var user in usernameLookup)
{
if (user.ClusterAccountVerified)
{
verifiedClusterAccount = true;
}
}
var model = new IndexViewModel
{
HasPassword = HasPassword(),
PhoneNumber = await UserManager.GetPhoneNumberAsync(userId),
ClusterAccountVerified = verifiedClusterAccount,
DawgTag = dawgTag,
TwoFactor = await UserManager.GetTwoFactorEnabledAsync(userId),
Logins = await UserManager.GetLoginsAsync(userId),
BrowserRemembered = await AuthenticationManager.TwoFactorBrowserRememberedAsync(userId)
};
var createdJobs = from j in db.GenomeModels
where j.CreatedBy.Equals(username)
select j;
ViewBag.JobsCreated = createdJobs.Count().ToString();
var finishedJobs = from j in db.GenomeModels
where j.CreatedBy.Equals(username)
where !string.IsNullOrEmpty(j.DownloadLink)
select j;
ViewBag.JobsFinished = finishedJobs.Count().ToString();
if (createdJobs.Count() != 0)
{
ViewBag.JobsFinishedStat = Convert.ToString(100 * finishedJobs.Count() / createdJobs.Count()) + "%";
}
else
{
ViewBag.JobsFinishedStat = "0%";
}
return(View(model));
}
}
