private bool SaveBacterialClone(SequencingPostModel postModel)
{
ValidateBacterialClone(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobBacterialClone = new UserJobBacterialClone();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobBacterialClone);
userJob.UserJobBacterialClone = userJobBacterialClone;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(postModel.PlateNames, userJob, userJob.JobType);
if (postModel.Strain != null && postModel.Strain.IsOther())
{
var strain = new Strain()
{
Name = postModel.NewStrain, Bacteria = postModel.Bacteria, Supplied = false
};
userJob.UserJobBacterialClone.Strain = strain;
}
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return(true);
}
return(false);
}
public IHttpActionResult PutUserJob(int id, UserJob userJob)
{
if (!ModelState.IsValid)
{
return(BadRequest(ModelState));
}
if (id != userJob.Id)
{
return(BadRequest());
}
try
{
repository.Put(userJob);
}
catch (DbUpdateConcurrencyException)
{
if (!UserJobExists(id))
{
return(NotFound());
}
else
{
throw;
}
}
return(StatusCode(HttpStatusCode.NoContent));
}
private bool SaveSublibrarySubmission(SequencingPostModel postModel)
{
ValidateSublibrarySubmission(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobSublibrary = new UserJobSublibrary();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobSublibrary);
userJob.UserJobSublibrary = userJobSublibrary;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(new List <string>()
{
userJob.Name
}, userJob, userJob.JobType);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return(true);
}
return(false);
}
private void PerformSyncThreadCycle()
{
Hyena.Log.Debug("Starting AppleDevice sync thread cycle");
var progressUpdater = new UserJob(Catalog.GetString("Syncing iPod"),
Catalog.GetString("Preparing to synchronize..."), GetIconNames());
progressUpdater.Register();
MediaDatabase.StartSync();
SyncTracksToAdd(progressUpdater);
SyncTracksToUpdate(progressUpdater);
SyncTracksToRemove(progressUpdater);
SyncTracksToPlaylists();
SyncDatabase(progressUpdater);
MediaDatabase.StopSync();
progressUpdater.Finish();
Hyena.Log.Debug("Ending AppleDevice sync thread cycle");
}
public ActionResult DeleteConfirmed(int id)
{
UserJob userJob = repo.GetJob(id);
repo.DeleteJob(userJob);
return(RedirectToAction("Index"));
}
public bool DeleteUserFromJob(UserJob assigned)
{
try
{
using (SqlConnection connection = new SqlConnection(connectionString))
{
connection.Open();
SqlCommand command = new SqlCommand(@"DELETE FROM (Id, title) VALUES(@id, @title);", connection);
command.Parameters.AddWithValue("@JobId", assigned.JobId);
command.Parameters.AddWithValue("@UserId", assigned.UserId);
command.ExecuteNonQuery();
if (assigned.JobId == null || assigned.UserId == null)
{
return(false);
}
else
{
return(true);
}
}
}
catch (SqlException E)
{
Console.WriteLine(E.Message);
return(false);
}
}
public ActionResult Create([Bind(Include = "JobTitle,JobDecription,JobType,Date,Latitude,Longitude")] JobViewModel _jobViewModel)
{
if (ModelState.IsValid)
{
//populate userJob object from database with viewmodel, add to database and redirect to index
UserJob userJob = new UserJob
{
JobTitle = _jobViewModel.JobTitle,
JobDescription = _jobViewModel.JobDecription,
JobType = _jobViewModel.JobType,
Date = DateTime.Now,
Latitude = _jobViewModel.Latitude,
Longitude = _jobViewModel.Longitude,
AspNetUser_Id = repo.GetUserId()
};
repo.PostJob(userJob);
return(RedirectToAction("Index"));
}
//if text field is empty or location isn't set, set viewbag message to display in the view
if (isNullOrEmpty(_jobViewModel.JobTitle) || isNullOrEmpty(_jobViewModel.JobDecription) ||
isNullOrEmpty(_jobViewModel.JobType))
{
ViewBag.error = "empty";
return(View(_jobViewModel));
}
else if (_jobViewModel.Latitude == 0.0 || _jobViewModel.Longitude == 0.0)
{
ViewBag.error = "location";
return(View(_jobViewModel));
}
return(View(_jobViewModel));
}
public bool AssignUserToJob(UserJob assigned)
{
try
{
using (SqlConnection connection = new SqlConnection(connectionString))
{
connection.Open();
SqlCommand command = new SqlCommand(@"INSERT INTO userJob (userID, job_Id) VALUES(@userId, @jobId);", connection);
command.Parameters.AddWithValue("@userId", assigned.UserId);
command.Parameters.AddWithValue("@jobId", assigned.JobId);
command.ExecuteNonQuery();
if (assigned.JobId == null || assigned.UserId == null)
{
return(false);
}
else
{
return(true);
}
}
}
catch (SqlException E)
{
Console.WriteLine(E.Message);
return(false);
}
}
public async Task <ActionResult <UserJob> > PostUserJob(UserJob userJob)
{
if (userJob.UserId != int.Parse(User.FindFirst(ClaimTypes.NameIdentifier).Value))
{
return(Unauthorized());
}
_context.UsersJobs.Add(userJob);
try
{
await _context.SaveChangesAsync();
}
catch (DbUpdateException)
{
if (UserJobExists(userJob.UserId, userJob.JobId))
{
return(Conflict());
}
else
{
throw;
}
}
return(CreatedAtAction("GetUserJob", new { id = userJob.UserId }, userJob));
}
public async Task <IActionResult> PutUserJob(int id, UserJob userJob)
{
if (id != int.Parse(User.FindFirst(ClaimTypes.NameIdentifier).Value))
{
return(Unauthorized());
}
if (id != userJob.UserId)
{
return(BadRequest());
}
_context.Entry(userJob).State = EntityState.Modified;
try
{
await _context.SaveChangesAsync();
}
catch (DbUpdateConcurrencyException)
{
if (!UserJobExists(id, userJob.JobId))
{
return(NotFound());
}
else
{
throw;
}
}
return(NoContent());
}
public async Task <ActionResult <UserJob> > PostUserJob(int userID, int jobID)
{
UserJob userJob = new UserJob
{
UserID = userID,
JobID = jobID
};
_context.UserJob.Add(userJob);
try
{
await _context.SaveChangesAsync();
}
catch (DbUpdateException)
{
if (UserJobExists(userJob.UserID))
{
return(Conflict());
}
else
{
throw;
}
}
return(CreatedAtAction("GetUserJob", new { id = userJob.UserID }, userJob));
}
public async Task <Unit> Handle(Command request,
CancellationToken cancellationToken)
{
var job = new Job
{
Id = request.Id,
Title = request.Title,
Description = request.Description,
Category = request.Category,
Date = request.Date,
City = request.City,
};
_context.Jobs.Add(job);
var user = await _context.Users.SingleOrDefaultAsync(x =>
x.UserName == _userAccessor.GetCurrentUsername());
var applicant = new UserJob
{
AppUser = user,
Job = job,
IsHost = true,
DateJoined = DateTime.Now
};
_context.UserJobs.Add(applicant);
var success = await _context.SaveChangesAsync() > 0;
if (success)
{
return(Unit.Value);
}
throw new Exception("Problem saving changes");
}
void SyncTracksToAdd(UserJob progressUpdater)
{
string message = Catalog.GetString("Adding track {0} of {1}");
int total = tracks_to_add.Count;
int i = 0;
while (tracks_to_add.Count > 0)
{
AppleDeviceTrackInfo track = null;
lock (sync_mutex) {
total = tracks_to_add.Count + i;
track = tracks_to_add.Dequeue();
}
try {
UpdateProgress(progressUpdater, message, ++i, total);
track.CommitToIpod(MediaDatabase);
track.Save(false);
tracks_map[track.TrackId] = track;
} catch (Exception e) {
Log.Error("Cannot save track to the Apple device", e);
}
}
if (total > 0)
{
OnTracksAdded();
OnUserNotifyUpdated();
}
}
void SyncTracksToRemove(UserJob progressUpdater)
{
string message = Catalog.GetString("Removing track {0} of {1}");
int total = tracks_to_remove.Count;
while (tracks_to_remove.Count > 0)
{
AppleDeviceTrackInfo track = null;
lock (sync_mutex) {
track = tracks_to_remove.Dequeue();
}
if (tracks_map.ContainsKey(track.TrackId))
{
tracks_map.Remove(track.TrackId);
}
try {
if (track.IpodTrack != null)
{
UpdateProgress(progressUpdater, message, total - tracks_to_remove.Count, total);
DeleteTrack(track.IpodTrack, true);
}
else
{
Log.Error("The ipod track was null");
}
} catch (Exception e) {
Log.Error("Cannot remove track from iPod", e);
}
}
SyncRemovalOfInvalidTracks(progressUpdater);
}
private void DisposeSyncUserJob()
{
if (sync_user_job != null)
{
sync_user_job.Finish();
sync_user_job = null;
}
}
private void OnIpodDatabaseSaveStarted(object o, EventArgs args)
{
DisposeSyncUserJob();
sync_user_job = new UserJob(Catalog.GetString("Syncing iPod"),
Catalog.GetString("Preparing to synchronize..."), GetIconNames());
sync_user_job.Register();
}
public UserJobModel(UserJob obj, bool isLoadJob = true)
{
ShareFunctions.CopyPropertiesTo <UserJob, UserJobModel>(obj, this);
if (isLoadJob)
{
Post = new JobPostModel(this.JobId);
}
}
public ActionResult DeleteConfirmed(int id)
{
UserJob userJob = db.UserJobs.Find(id);
db.UserJobs.Remove(userJob);
db.SaveChanges();
return(RedirectToAction("Index"));
}
private void OnSubmissionEnd(object source, EventArgs args)
{
if (scrobble_job != null)
{
scrobble_job.Finish();
scrobble_job = null;
}
}
public bool Update(UserJob data)
{
string id = $"{data.id_user_job}";
data.id_user_job = string.Empty;
data.ngay_sua = XMedia.XUtil.TimeInEpoch(DateTime.Now);
return(Update(_default_index, data, id));
}
public ActionResult Edit([Bind(Include = "Id,JobTitle,JobDecription,JobType,Date,Latitude,Longitude,AspNetUser_Id")] UserJob userJob)
{
if (ModelState.IsValid)
{
repo.PutJob(userJob);
return(RedirectToAction("Index"));
}
return(View(userJob));
}
public bool UpdateThuocTinh(UserJob data)
{
string id = $"{data.id_user_job}";
data.id_user_job = string.Empty;
data.ngay_sua = XMedia.XUtil.TimeInEpoch(DateTime.Now);
var re = client.Update <UserJob, object>(id, u => u.Doc(new { ngay_sua = data.ngay_sua, thuoc_tinh = data.thuoc_tinh }));
return(re.Result == Result.Updated || re.Result == Result.Noop);
}
public ActionResult Edit([Bind(Include = "UserJobID,JobID,UserID")] UserJob userJob)
{
if (ModelState.IsValid)
{
db.Entry(userJob).State = EntityState.Modified;
db.SaveChanges();
return(RedirectToAction("Index"));
}
return(View(userJob));
}
public IHttpActionResult PostUserJob(UserJob userJob)
{
if (!ModelState.IsValid)
{
return(BadRequest(ModelState));
}
repository.Post(userJob);
return(CreatedAtRoute("DefaultApi", new { id = userJob.Id }, userJob));
}
public IHttpActionResult GetUserJob(int id)
{
UserJob userjob = repository.Get(id);
if (userjob == null)
{
return(NotFound());
}
return(Ok(userjob));
}
public ActionResult Create([Bind(Include = "UserJobID,JobID,UserID")] UserJob userJob)
{
if (ModelState.IsValid)
{
db.UserJobs.Add(userJob);
db.SaveChanges();
return(RedirectToAction("Index"));
}
return(View(userJob));
}
private void OnFinished(object o, EventArgs args)
{
if (user_job != null)
{
user_job.CancelRequested -= OnCancelRequested;
user_job.Finished -= OnFinished;
user_job = null;
}
source.UnlockAllTracks();
}
public void UpdateUserJob(UserJob Entity)
{
try
{
_userJobRepository.Update(Entity);
}
catch (IntegratorException e)
{
throw e;
}
}
private bool SaveColonyPicking(QbotPostModel postModel)
{
ValidateColonyPicking(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobColonyPicking = new UserJobQbotColonyPicking();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobColonyPicking);
userJob.UserJobQbotColonyPicking = userJobColonyPicking;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
if (postModel.Strain.IsOther())
{
var strain = new Strain()
{
Name = postModel.NewStrain, Bacteria = postModel.Bacteria, Supplied = false
};
userJob.UserJobQbotColonyPicking.Strain = strain;
}
if (postModel.Vector.IsOther())
{
var vector = new Vector()
{
Name = postModel.NewVector, VectorType = postModel.VectorType, Antibiotic1 = postModel.Antibiotic1, Antibiotic2 = postModel.Antibiotic2
};
userJob.UserJobQbotColonyPicking.Vector = vector;
}
// add plate
var stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.QpWebSubmittedPlates);
var barcode = new Barcode()
{
Stage = stage
};
var userJobPlate = new UserJobPlate()
{
Name = userJob.Name
};
userJobPlate.AddBarcode(barcode);
userJob.AddUserJobPlates(userJobPlate);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return(true);
}
return(false);
}
public async Task StartMonitoring()
{
var users = await _userRepository.GetUsers().ConfigureAwait(false);
foreach (var user in users)
{
var userJob = new UserJob(user, _twitchIntegration, _streamHealthLogger);
userJob.Run();
_userJobs.Add(userJob);
_logger.LogInformation($"Started job for {user.Username}");
}
}
public void AdvanceAllBarcodes(IRepositoryFactory repositoryFactory, UserJob userJob, Stage stage)
{
var barcodes = userJob.UserJobPlates.SelectMany(a => a.Barcodes).Where(a => a.Stage == stage && !a.Done);
if (barcodes.Any())
{
foreach(var bc in barcodes)
{
AdvanceStage(repositoryFactory, bc, userJob);
}
}
}
/// <summary>
/// Adds the plates necessary for the original submission
/// </summary>
/// <param name="plateNames"></param>
/// <param name="userJob"></param>
private void AddPlates(List<string> plateNames, UserJob userJob, JobType jobType)
{
// figure out the stage
Stage stage = null;
switch(jobType.Id)
{
case (int)JobTypeIds.BacterialClone:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.BcWebSubmittedPlates);
break;
case (int)JobTypeIds.PCRProduct:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.PcrWebSubmittedPlates);
break;
case (int)JobTypeIds.UserRunSequencing:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.UrsWebSubmittedPlates);
break;
case (int)JobTypeIds.PurifiedDna:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.PdWebSubmittedPlates);
break;
case (int)JobTypeIds.Sublibrary:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.SlWebSubmittedPlates);
break;
}
if (stage == null)
{
throw new ArgumentException("JobType");
}
foreach(var name in plateNames)
{
var plate = new UserJobPlate() {Name = name};
var barcode = new Barcode() {Stage = stage};
plate.AddBarcode(barcode);
userJob.AddUserJobPlates(plate);
}
}
private bool SaveBacterialClone(SequencingPostModel postModel)
{
ValidateBacterialClone(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobBacterialClone = new UserJobBacterialClone();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobBacterialClone);
userJob.UserJobBacterialClone = userJobBacterialClone;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(postModel.PlateNames, userJob, userJob.JobType);
if (postModel.Strain != null && postModel.Strain.IsOther())
{
var strain = new Strain() { Name = postModel.NewStrain, Bacteria = postModel.Bacteria, Supplied = false };
userJob.UserJobBacterialClone.Strain = strain;
}
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
private bool SaveSublibrarySubmission(SequencingPostModel postModel)
{
ValidateSublibrarySubmission(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobSublibrary = new UserJobSublibrary();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobSublibrary);
userJob.UserJobSublibrary = userJobSublibrary;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(new List<string>() {userJob.Name}, userJob, userJob.JobType);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
private bool SaveUserRunSubmission(SequencingPostModel postModel)
{
ValidateUserRunSubmission(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobUserRun = new UserJobUserRun();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobUserRun);
userJob.UserJobUserRun = userJobUserRun;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(postModel.PlateNames, userJob, userJob.JobType);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
public void AdvanceStage(IRepositoryFactory repositoryFactory, Barcode barcode, UserJob userJob)
{
// barcode is complete and cannot be advanced
if (barcode.Stage.IsComplete) return;
var jobType = userJob.JobType;
var stage = barcode.Stage;
var plate = barcode.UserJobPlate;
// by default only insert one new barcode
var subPlates = 1;
// jobs with large plate, gets broken down to 4 barcodes
if (_largeplateJobs.Contains(jobType.Id) && userJob.PlateType == PlateTypes.ThreeEightyFour && stage.Order == 2)
{
subPlates = 4;
}
Primer primer1 = barcode.Primer;
Primer primer2 = null;
var directional = false;
// if it's directional, you need a forward and back for each sub plate to generate
if (_directionalJobs.Contains(jobType.Id))
{
// bacterial clone, 2nd stage, take the direction
if (jobType.Id == (int)JobTypeIds.BacterialClone && stage.Order == 3 && userJob.UserJobBacterialClone.SequenceDirection == SequenceDirection.Backward)
{
directional = true;
primer1 = userJob.UserJobBacterialClone.Primer1;
primer2 = userJob.UserJobBacterialClone.Primer2;
}
// frankly, I think this was old code that isn't used any more
// pcr and purified dna take the direction at 1st stage
if ((jobType.Id == (int)JobTypeIds.PCRProduct || jobType.Id == (int)JobTypeIds.PurifiedDna) && stage.Order == 2 && userJob.UserJobDna.SequenceDirection == SequenceDirection.Backward)
{
directional = true;
primer1 = userJob.UserJobDna.Primer1;
primer2 = userJob.UserJobDna.Primer2;
}
}
// load the next stage
var nextStage = jobType.Stages.First(a => a.Order == stage.Order + 1);
for (var i = 0; i < subPlates; i++)
{
// write the first plate
var newBarcode1 = new Barcode() { SourceBarcode = barcode, Stage = nextStage, Primer = primer1, SubPlateId = i + 1};
plate.AddBarcode(newBarcode1);
if (directional)
{
var newBarcode2 = new Barcode() { SourceBarcode = barcode, Stage = nextStage, Primer = primer2, SubPlateId = i + 1 };
plate.AddBarcode(newBarcode2);
}
}
barcode.Done = true;
repositoryFactory.UserJobPlateRepository.EnsurePersistent(plate);
userJob.LastUpdate = DateTime.Now;
repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
}
