private void CleanupDatabase()
{
var log = Log.GetLogger();
var cfg = CapiConfig.GetConfig();
if (cfg == null)
{
throw new ApplicationException("Unable to find config file.");
}
var dbBroker = new DbBroker(cfg.AgentDbConnectionString);
if (dbBroker.Database.EnsureCreated())
{
log.Info("Database not found, so it has been created.");
}
else
{
log.Info("Database found.");
}
if (!dbBroker.Database.CanConnect())
{
log.Error("Could not connect to database using string: " + cfg.AgentDbConnectionString);
}
else
{
log.Info("DB Connection established");
}
try
{
log.Info("DB Connection good? " + dbBroker.Database.CanConnect());
var failedCases = dbBroker.GetCaseByStatus("Processing");
foreach (var c in failedCases)
{
var tmp = c;
tmp.Status = "Pending";
dbBroker.Attempts.Update(tmp);
dbBroker.SaveChanges();
}
var failedJobs = dbBroker.GetJobByStatus("Processing");
foreach (var j in failedJobs)
{
var tmp = j;
tmp.Status = "Failed";
dbBroker.Jobs.Update(tmp);
dbBroker.SaveChanges();
}
}
catch (Exception e)
{
log.Error("Error while accesing database. If this is due to an incompatible schema, maybe try wiping the database and starting again?");
log.Error(e);
}
}
/// <summary>
/// Builds a Job using details in Recipe
/// </summary>
/// <param name="recipe">Contains details of studies to process, source and destinations</param>
/// <returns></returns>
public Job Build(Recipe recipe, Attempt attempt)
{
if (string.IsNullOrEmpty(recipe.CurrentAccession))
{
recipe.CurrentAccession = attempt.CurrentAccession;
}
// TODO: We probably don't need to replace the prior accession since the attempt shouldn't have anything at this stage.
if (string.IsNullOrEmpty(recipe.PriorAccession))
{
recipe.PriorAccession = attempt.PriorAccession;
}
// Setup out dicom service.
var dicomSource = CreateDicomSource(recipe.SourceAet);
// Get patient id
var patientId = GetPatientId(recipe, dicomSource);
// A list of all studies for the patient.
// TODO: I don't love the fact that we can't just use the patient ID which we should have above.
// But this code is defensive so I don't want to change it and introduce more bugs.
var allStudiesForPatient =
GetStudiesForPatient(patientId, recipe.PatientFullName, recipe.PatientBirthDate, dicomSource);
// Update attempt in DB
@attempt.PatientId = recipe.PatientId;
_context.Attempts.Update(@attempt);
_context.SaveChanges();
// If there are no studies, have a cry.
if (allStudiesForPatient.Count < 1)
{
throw new StudyNotFoundException(
$"No studies for patient [{recipe.PatientFullName}] could be found in node AET: [{dicomSource.RemoteNode.AeTitle}]");
}
// Update patient ID in DB for a second time?
@attempt.PatientId = allStudiesForPatient.FirstOrDefault().PatientId;
@attempt.PatientFullName = allStudiesForPatient.FirstOrDefault().PatientsName;
@attempt.PatientBirthDate = allStudiesForPatient.FirstOrDefault().PatientBirthDate.ToString("yyyyMMdd");
_context.Attempts.Update(@attempt);
_context.SaveChanges();
// Update the recipe with all the details for the patient?
recipe = UpdateRecipeWithPatientDetails(recipe, allStudiesForPatient);
// Find Current Study
_log.Info("Finding current series using recipe provided...");
var currentDicomStudy = GetCurrentDicomStudy(recipe, allStudiesForPatient, dicomSource);
// Update case in DB with patient name and DOB
@attempt.PatientFullName = recipe.PatientFullName;
@attempt.PatientBirthDate = recipe.PatientBirthDate;
_context.Attempts.Update(@attempt);
_context.SaveChanges();
// If we don't have a matching study for current have a cry.
if (currentDicomStudy == null ||
currentDicomStudy.Series.Count == 0)
{
throw new StudyNotFoundException("No workable series were found for accession");
}
// Update attempt with accession number.
@attempt.CurrentAccession = currentDicomStudy.AccessionNumber;
@attempt.CurrentSeriesUID = currentDicomStudy.Series.FirstOrDefault().SeriesInstanceUid;
_context.Attempts.Update(@attempt);
_context.SaveChanges();
// Create a new job based on the recipe.
var job = new Job(recipe, attempt);
job.Status = "Pending";
job.AttemptId = attempt.Id;
// Setup temp directory for images.
var capiConfig = CapiConfig.GetConfig();
try
{
job.ProcessingFolder = Path.GetFullPath(Path.Combine(capiConfig.ImagePaths.ImageRepositoryPath, job.Attempt.CurrentAccession + "-" + job.Id));
}
catch (Exception ex)
{
Log.GetLogger().Error($"{capiConfig.ImagePaths.ImageRepositoryPath} may not be a valid path.");
Log.GetLogger().Error(ex.Message);
}
try
{
job.ResultSeriesDicomFolder = Path.GetFullPath(Path.Combine(job.ProcessingFolder, Results));
}
catch (Exception ex)
{
Log.GetLogger().Error($"{Path.Combine(job.ProcessingFolder, Results)} may not be a valid path.");
Log.GetLogger().Error(ex.Message);
}
try
{
job.PriorReslicedSeriesDicomFolder = Path.GetFullPath(Path.Combine(job.ProcessingFolder, PriorResliced));
}
catch (Exception ex)
{
Log.GetLogger().Error($"{Path.Combine(job.ProcessingFolder, PriorResliced)} may not be a valid path.");
Log.GetLogger().Error(ex.Message);
}
try
{
job.ReferenceSeriesDicomFolder = Path.GetFullPath(GetReferenceSeriesForRegistration(job, allStudiesForPatient, dicomSource));
}
catch (Exception ex)
{
Log.GetLogger().Info($"{GetReferenceSeriesForRegistration(job, allStudiesForPatient, dicomSource)} may not be a valid path.");
}
// Find Prior Study (Floating)
_log.Info("Finding prior series using recipe provided...");
var studyFixedIndex = allStudiesForPatient.IndexOf(currentDicomStudy);
var priorDicomStudy =
GetPriorDicomStudy(recipe, studyFixedIndex, allStudiesForPatient, dicomSource);
// If we couldn't find the prior study, have a cry.
if (priorDicomStudy == null)
{
throw new StudyNotFoundException("No prior workable series were found");
}
// Otherwise update the attempt
job.Attempt.PriorAccession = priorDicomStudy.AccessionNumber;
job.Attempt.PatientId = currentDicomStudy.PatientId;
// Update attempt with prior accession details.
@attempt.PriorAccession = priorDicomStudy?.AccessionNumber;
@attempt.PriorSeriesUID = priorDicomStudy?.Series?.FirstOrDefault()?.SeriesInstanceUid;
@attempt.SourceAet = recipe.SourceAet;
@attempt.DestinationAet = JsonConvert.SerializeObject(recipe.OutputSettings.DicomDestinations);
@job.RecipeString = JsonConvert.SerializeObject(job.Recipe, new CapiConfigJsonConverter());
_context.Attempts.Update(@attempt);
_context.Jobs.Update(@job);
_context.SaveChanges();
// If both current and prior are found, save them to disk for processing
_log.Info("Saving current series to disk...");
try
{
job.CurrentSeriesDicomFolder =
SaveDicomFilesToFilesystem(currentDicomStudy, job.ProcessingFolder, Current, dicomSource);
}
catch (Exception ex)
{
_log.Error("Failed to save current series dicom files to disk.", ex);
throw ex;
}
if (Directory.EnumerateFiles(job.CurrentSeriesDicomFolder).Count() < 1)
{
_log.Error($"Could not find any dicom files for current series in directory {job.CurrentSeriesDicomFolder}. Check that Accession exists and you can perform a CMOVE to this machine.");
throw new Exception($"Could not find any dicom files for current series in directory {job.CurrentSeriesDicomFolder}. Check that Accession exists and you can perform a CMOVE to this machine.");
}
_log.Info($"Saved current series to [{job.CurrentSeriesDicomFolder}]");
_log.Info("Saving prior series to disk...");
try
{
job.PriorSeriesDicomFolder = SaveDicomFilesToFilesystem(
priorDicomStudy, job.ProcessingFolder, Prior, dicomSource);
}
catch (Exception ex)
{
_log.Error("Failed to save prior series dicom files to disk.", ex);
throw;
}
if (Directory.EnumerateFiles(job.PriorSeriesDicomFolder).Count() < 1)
{
_log.Error($"Could not find any dicom files for prior series in directory {job.PriorSeriesDicomFolder}. Check that Accession exists and you can perform a CMOVE to this machine.");
throw new Exception($"Could not find any dicom files for prior series in directory {job.PriorSeriesDicomFolder}. Check that Accession exists and you can perform a CMOVE to this machine.");
}
_log.Info($"Saved prior series to [{job.PriorReslicedSeriesDicomFolder}]");
// All done.
return(job);
}
