public ComparisonViewModelTestConductor(GenomeModel a = null, GenomeModel b = null)
{
View = new ComparisonViewModel(
Favourites.Object,
a ?? TestGenomeModel.Create(),
b);
}
// GET: GenomeAssembly/Details/5
public ActionResult Details(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
GenomeModel genomeModel = db.GenomeModels.Find(id);
if (genomeModel == null)
{
return(HttpNotFound());
}
string currentUser = User.Identity.Name;
// Only let the user that created the job view that job.
if (genomeModel.CreatedBy.Equals(currentUser))
{
if (!string.IsNullOrEmpty(genomeModel.DownloadLink))
{
// We need to display the download link for the user which is set in CheckJobStatus.UploadData() and stored in the model
// under DownloadLink.
}
return(View(genomeModel));
}
else
{
return(RedirectToAction("DetailsPermissionError", "Error"));
}
}
public static bool IsAssemblyFinished(this GenomeModel genomeModel)
{
int assemblersFinished = 0;
if (genomeModel.UseMasurca)
{
if (genomeModel.MasurcaCurrentStep.Equals(StepDescriptions.GetMasurcaStepList().Last().step))
{
assemblersFinished++;
}
}
if (genomeModel.UseSGA)
{
}
if (genomeModel.UseWGS)
{
}
if (assemblersFinished.Equals(genomeModel.NumberOfAssemblers))
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Updates the status of the masurca assembler. If it has either errored out (-1) or is completed (last step), it will not change the status.
/// </summary>
/// <param name="client">The current SSH client session.</param>
/// <param name="genomeModel">The model of the particular job.</param>
private static void CheckMasurcaStep(SshClient client, GenomeModel genomeModel)
{
if (string.IsNullOrEmpty(ErrorHandling.error) &&
!genomeModel.MasurcaCurrentStep.Equals(-1) &&
!genomeModel.MasurcaCurrentStep.Equals(StepDescriptions.GetMasurcaStepList().Last().step))
{
if (LinuxCommands.DirectoryHasFiles(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed)))
{
int currentMasurcaStep = LinuxCommands.GetCurrentStep(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed), StepDescriptions.GetMasurcaStepList());
// Provided we didn't encounter an error, set the status of masurca and the job.
if (currentMasurcaStep != -1)
{
genomeModel.MasurcaCurrentStep = currentMasurcaStep;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), currentMasurcaStep);
}
else
{
StepDescriptions.SetMasurcaError(client, genomeModel);
}
}
// Either masurca hasn't started or it has but no files have been created yet.
else
{
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
}
}
}
private IEnumerable <SnpViewModel> MakeSnpViewModels(GenomeModel a, GenomeModel b)
{
if (b == null)
{
foreach (var aa in a.Snp)
{
yield return(MakeSnpViewModel(aa, null));
}
yield break;
}
// SNP in genome A and SNP in both genome A and B.
foreach (var aa in a.Snp)
{
SnpModel bb;
b.Snp.TryGetById(aa.Id, out bb);
yield return(MakeSnpViewModel(aa, bb));
}
// SNP only in genome B.
foreach (var bb in b.Snp)
{
SnpModel _;
if (a.Snp.TryGetById(bb.Id, out _))
{
continue;
}
yield return(MakeSnpViewModel(null, bb));
}
}
/// <summary>
/// Initializes a new instance of the <see cref="ComparisonViewModel"/> class.
/// </summary>
/// <param name="favouritesManager">The favourites manager.</param>
/// <param name="a">The first gneome to compare.</param>
/// <param name="b">The optional second genome to compare, can be <see langword="null"/>.</param>
/// <exception cref="System.ArgumentNullException">
/// Thrown if <paramref name="favouritesManager"/> or <paramref name="a"/> is <see langword="null"/>.
/// </exception>
public ComparisonViewModel(IFavouritesManager favouritesManager, GenomeModel a, GenomeModel b = null)
{
Guard.IsNotNull(favouritesManager, nameof(favouritesManager));
Guard.IsNotNull(a, nameof(a));
_favouritesManager = favouritesManager;
Snp = new SnpViewModelCollection(MakeSnpViewModels(a, b));
}
public ActionResult Details(int id, string command)
{
GenomeModel genomeModel = db.GenomeModels.Find(id);
if (command == "Update Status" && string.IsNullOrEmpty(genomeModel.DownloadLink))
{
JobMaintenance.UpdateStatus(genomeModel);
}
if (command == "Cancel Job")
{
// Add a method in JobMaintenance that reflects cancelling a job. Best place for it.
}
db.SaveChanges();
return(View(genomeModel));
}
/// <summary>
/// Sets default values if the user decided not to enter any information for optional values in the wizard.
/// </summary>
/// <param name="genomeModel">The model data for a particular job.</param>
/// <returns>Returns the new job model with the default values.</returns>
public static GenomeModel SetDefaultMasurcaValues(GenomeModel genomeModel)
{
// If they don't have jump reads.
if (genomeModel.JumpReads == false)
{
genomeModel.JumpLength = 0;
}
// If they don't have paired-end reads.
if (genomeModel.PEReads == false)
{
genomeModel.PairedEndLength = 0;
}
if (genomeModel.MasurcaMean == null)
{
genomeModel.MasurcaMean = 180;
}
if (genomeModel.MasurcaStdev == null)
{
genomeModel.MasurcaStdev = 20;
}
// We don't specify anything here. If it is null, we set it to AUTO in the masurca method of the config builder.
if (genomeModel.MasurcaGraphKMerValue == null)
{
if (genomeModel.MasurcaKMerErrorCount == null)
{
genomeModel.MasurcaKMerErrorCount = 1;
}
}
if (genomeModel.MasurcaThreadNum == null)
{
genomeModel.MasurcaThreadNum = 20;
}
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
return(genomeModel);
}
/// <summary>
/// Updates the status of the job by appropriately increasing the step and changing the status.
/// </summary>
/// <param name="genomeModel">The model that represents the current job.</param>
/// <param name="hasError">If there is an error during execution, it will set the current status of the job to an error state and sets the step number to the final step.</param>
/// <param name="customErrorMsg">Instead of the default error messages associated with each step, you may list your own.</param>
public static void NextStep(this GenomeModel genomeModel, bool hasError = false, string customErrorMsg = "")
{
if (hasError)
{
if (string.IsNullOrWhiteSpace(customErrorMsg))
{
genomeModel.OverallStatus = GetOverallStepErrors()[genomeModel.OverallCurrentStep].ToString();
}
else
{
genomeModel.OverallStatus = customErrorMsg;
}
}
else
{
genomeModel.OverallStatus = GetOverallStepList()[++genomeModel.OverallCurrentStep].ToString();
}
}
public void SetupLoadAsyncToReturn(Expression <Func <string, bool> > match, GenomeModel returnValue)
{
_mock.Setup(x => x.LoadAsync(It.Is(match))).Returns(Task.FromResult(returnValue));
}
/// <param name="genomeModel">The model data of the current job.</param>
/// <param name="dataSources">A stored list of strings containing the location(s) of the user's data set.</param>
/// <param name="seed">Seed value for a unique name for the job.</param>
public JobBuilder(GenomeModel genomeModel, List <string> dataSources, int seed)
{
this.genomeModel = genomeModel;
this.seed = seed;
this.dataSources = dataSources;
}
public ActionResult Create(GenomeModel genomeModel)
{
if (ModelState.IsValid)
{
// TODO: Consider the JELLYFISH SIZE. Rec size is est_genome_size * estimated coverage. (This should be done in Javascript).
// Should that be a field that we include in the model so we can calculate a safe size or just
// have them do it? I think just have them do it with a tooltip and make it a required field.
try
{
#region Set General Information
HelperMethods.SetDefaultMasurcaValues(genomeModel);
genomeModel.OverallCurrentStep = 1;
genomeModel.OverallStatus = StepDescriptions.INITIAL_STEP;
genomeModel.NumberOfAssemblers = HelperMethods.NumberOfAssemblers(genomeModel.UseMasurca, genomeModel.UseSGA, genomeModel.UseWGS);
// TODO: Potentially add the model to the DB now with junk data to reserve the UUID so we don't have to use a SEED value at all. This
// reduces the potential of something going wrong and two people ending up with a race condition or something.
genomeModel.CreatedBy = User.Identity.Name;
// TODO: Need to look into this to see about a translation to display to a user rather than the UK time it gives.
genomeModel.CreatedDate = DateTime.UtcNow;
#endregion
#region Create Scripts
List <string> dataSources = HelperMethods.ParseUrlString(genomeModel.DataSource);
Random rand = new Random();
int seed = rand.Next(198, 1248712);
JobBuilder builder = new JobBuilder(genomeModel, dataSources, seed);
builder.GenerateConfigs();
genomeModel.Seed = builder.seed; // Set seed value here so we know it is 100% definitely set.
#endregion
#region Connect To BigDog and Test Data Connection
string badUrl = HelperMethods.TestJobUrls(genomeModel.SSHUser, genomeModel.SSHPass, genomeModel.DataSource);
if (string.IsNullOrEmpty(badUrl) && string.IsNullOrEmpty(ErrorHandling.error))
{
/// We can instead pass in the SEED variable which will be used to reference the method in Locations to grab the correct file(s).
/// This is the ideal solution which will be implemented only once we know that the system works with the direct URL.
builder.CreateJob();
// No error so proceed.
if (ErrorHandling.NoError())
{
db.GenomeModels.Add(genomeModel);
db.SaveChanges();
return(RedirectToAction("Details", new { id = genomeModel.uuid }));
}
// Redisplay the data and display the error.
else
{
genomeModel.JobError = "We encountered an error while trying to submit your job. The following is the error we encountered: " + ErrorHandling.error;
return(View(genomeModel));
}
}
// Redisplay the data and display the error.
else
{
genomeModel.JobError = "There was an error with the URLs provided. We weren't able to locate or download at least"
+ " one of your files. The file we had a problem with was: " + badUrl + ". Please make sure you typed the URL correctly"
+ " and it is accessible. If this is in error, please contact an administrator promptly with the details.";
if (!string.IsNullOrEmpty(ErrorHandling.error))
{
genomeModel.JobError = string.Concat(genomeModel.JobError, " The following is additional error information that we encountered: " + ErrorHandling.error);
}
return(View(genomeModel));
}
#endregion
}
catch (Exception e)
{
genomeModel.JobError = "There has been an uncaught error. " + e;
}
}
return(View(genomeModel));
}
/// <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;
}
}
}
/// <inheritdoc/>
public Task<GenomeModel> LoadAsync(string path)
{
return Task.Run(() => GenomeModel.Load(path));
}
public static void SetMasurcaError(SshClient client, GenomeModel genomeModel)
{
genomeModel.MasurcaCurrentStep = -1;
genomeModel.MasurcaStatus = LinuxCommands.GetMasurcaError(client, genomeModel.Seed);
}
