public void ProcessModelToViewModel_SetsPatientId()
{
var sut = new MeningoIsolateViewModelMappingAction();
var isolateViewModel = new MeningoIsolateViewModel();
var isolate = CreateEmptyIsolate();
isolate.Sending.Patient.PatientId = 123;
sut.Process(isolate, isolateViewModel);
isolateViewModel.PatientId.Should().Be(123);
}
public void ProcessViewModelToModel_NoGrowthAtAll_SetFieldMeningoMaterialToNoGrowthExceptForNativeMaterial(MeningoMaterial currentMaterial, MeningoMaterial expectedMaterial)
{
var sut = new MeningoIsolateViewModelMappingAction();
var isolateViewModel = new MeningoIsolateViewModel();
var isolate = CreateEmptyIsolate();
isolate.Sending.Material = currentMaterial;
sut.Process(isolateViewModel, isolate);
isolate.Sending.Material.Should().Be(expectedMaterial);
}
public void ProcessModelToViewModel_OtherNonInvasiveSamplingLocation()
{
var sut = new MeningoIsolateViewModelMappingAction();
var isolateViewModel = new MeningoIsolateViewModel();
var isolate = CreateEmptyIsolate();
isolate.Sending.SamplingLocation = MeningoSamplingLocation.OtherNonInvasive;
isolate.Sending.OtherNonInvasiveSamplingLocation = "Noninvasive Location";
sut.Process(isolate, isolateViewModel);
isolateViewModel.SamplingLocation.Should().Be("Noninvasive Location");
}
public void ProcessModelToViewModel_ConvertsEnumValuesToDescription()
{
var sut = new MeningoIsolateViewModelMappingAction();
var isolateViewModel = new MeningoIsolateViewModel();
var isolate = CreateEmptyIsolate();
isolate.Sending.SamplingLocation = MeningoSamplingLocation.BloodAndLiquor;
isolate.Sending.Material = MeningoMaterial.IsolatedDna;
sut.Process(isolate, isolateViewModel);
isolateViewModel.SamplingLocation.Should().Be("Blut und Liquor");
isolateViewModel.Material.Should().Be("Isolierte DNA");
isolateViewModel.Invasive.Should().Be("Ja");
}
public void ProcessModelToViewModel_PopulatesSenderData()
{
var sut = new MeningoIsolateViewModelMappingAction();
var isolateViewModel = new MeningoIsolateViewModel();
var isolate = CreateEmptyIsolate();
DbMock.Senders.Find(1).Name = "Test Sender";
DbMock.Senders.Find(1).PostalCode = "12345";
DbMock.Senders.Find(1).City = "The City";
DbMock.Senders.Find(1).StreetWithNumber = "Long Street 123456";
sut.Process(isolate, isolateViewModel);
isolateViewModel.SenderName.Should().Be("Test Sender");
isolateViewModel.SenderCity.Should().Be("12345 The City");
isolateViewModel.SenderStreet.Should().Be("Long Street 123456");
}
static void Main(string[] args)
{
Database.SetInitializer(new MigrateDatabaseToLatestVersion <ApplicationDbContext, Configuration>());
var connectionString =
$"Provider=Microsoft.ACE.OLEDB.12.0;Data Source={args[0]};Jet OLEDB:Database Password={args[1]}";
Mapper.Initialize(cfg =>
{
cfg.CreateMap <object, MeningoSamplingLocation>()
.ConvertUsing <AccessMeningoSamplingLocationConverter>();
cfg.CreateMap <Dictionary <string, object>, MeningoPatient>()
.ConvertUsing <AccessMeningoPatientConverter>();
cfg.CreateMap <Dictionary <string, object>, MeningoSending>()
.ConvertUsing <AccessMeningoSendingConverter>();
cfg.CreateMap <Dictionary <string, object>, MeningoIsolate>()
.ConvertUsing <AccessMeningoIsolateConverter>();
});
var selectSamplingLocations = "SELECT * FROM tbl_isol_mat";
foreach (var meningoSamplingLocation in LoadAndConvert <MeningoSamplingLocation>(connectionString, selectSamplingLocations, "isol_mat_nr"))
{
Console.WriteLine(meningoSamplingLocation);
}
var selectPatients =
$"SELECT {PatientAccessTable}.* FROM {PatientAccessTable} INNER JOIN {StemAccessTable} ON {PatientAccessTable}.patnr = {StemAccessTable}.patnr"; // "WHERE Year(eing_dat)=2019";
var patientFields = new[]
{
"initialen", "geb_dat", "geschlecht", "plz", "wohnort", "bundeslandnr", "meningitis", "sepsis", "wfs",
"sonst_sympt", "k_sympt", "patnr", "n_spez", "and_inv_erkr", "grunderkr", "notizen"
};
Dictionary <int, int> patientIdLookup = new Dictionary <int, int>();
var patients = LoadAndConvert <MeningoPatient>(connectionString, selectPatients, patientFields).ToList();
var validationFailed = false;
foreach (var patient in patients)
{
var validator = new MeningoPatientValidator();
if (validator.Validate(patient).Errors.Any())
{
Console.WriteLine($"Validierung für Patient {patient.PatientId} fehlgeschlagen:");
foreach (var error in validator.Validate(patient).Errors)
{
Console.WriteLine(error.ErrorMessage);
validationFailed = true;
}
}
}
var sendings = LoadSendings(connectionString).ToList();
foreach (var sending in sendings)
{
var validator = new MeningoSendingValidator();
if (validator.Validate(sending).Errors.Any())
{
Console.WriteLine("");
Console.WriteLine($"Validierung für Einsendung {sending.MeningoSendingId} fehlgeschlagen:");
foreach (var error in validator.Validate(sending).Errors)
{
Console.WriteLine(error.ErrorMessage);
if (error.ErrorMessage.Contains("Anderer Entnahmeort") && error.ErrorMessage.Contains("darf nicht leer sein"))
{
continue;
}
validationFailed = true;
}
}
}
if (validationFailed)
{
return;
}
var currentSeed = Context.MeningoPatients.Max(p => p.PatientId);
foreach (var patient in patients)
{
var oldId = patient.PatientId;
if (!patientIdLookup.ContainsKey(oldId))
{
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoPatients], RESEED, {0})", patient.PatientId - 1));
Console.WriteLine(patient);
Context.MeningoPatients.Add(patient);
new ApplicationDbContextWrapper(Context).SaveChanges();
if (patient.PatientId != oldId)
{
Console.WriteLine($"ERROR: Patient ID mismatch old: {oldId}, new: {patient.PatientId}");
return;
}
patientIdLookup.Add(oldId, patient.PatientId);
}
}
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoPatients], RESEED, {0})", currentSeed));
var sendingLookup = new Dictionary <int, MeningoSending>();
foreach (var sending in sendings)
{
var oldId = sending.MeningoSendingId;
sendingLookup.Add(oldId, sending);
//Console.WriteLine(sending);
}
var currentIsolateSeed = Context.MeningoIsolates.Max(i => i.MeningoIsolateId);
var currentSendingSeed = Context.MeningoSendings.Max(s => s.MeningoSendingId);
foreach (var isolate in LoadIsolates(connectionString))
{
var sending = sendingLookup[isolate.MeningoSendingId];
isolate.Sending = sending;
isolate.Sending.Patient = Context.MeningoPatients.Find(sending.MeningoPatientId);
if (Regex.Match(sending.LaboratoryNumber, "NR\\d+/\\d+").Success)
{
var noPrefix = sending.LaboratoryNumber.Replace("NR", "");
var labNumberAndYear = noPrefix.Split('/');
var remark = "Nativmaterial: " + sending.LaboratoryNumber;
isolate.YearlySequentialIsolateNumber = (-1) * int.Parse(labNumberAndYear[0]);
isolate.Year = 2000 + int.Parse(labNumberAndYear[1]);
isolate.Remark = string.IsNullOrEmpty(isolate.Remark) ? remark : "\n" + remark;
// Special handling for SerogroupPCR on native material
var serogroupPcr = isolate.SerogroupPcr;
if (serogroupPcr != MeningoSerogroupPcr.NotDetermined)
{
switch (serogroupPcr)
{
case MeningoSerogroupPcr.B:
isolate.CsbPcr = NativeMaterialTestResult.Positive;
break;
case MeningoSerogroupPcr.C:
isolate.CscPcr = NativeMaterialTestResult.Positive;
break;
case MeningoSerogroupPcr.W:
isolate.CswyPcr = NativeMaterialTestResult.Positive;
isolate.CswyAllele = CswyAllel.Allele1;
break;
case MeningoSerogroupPcr.Y:
isolate.CswyPcr = NativeMaterialTestResult.Positive;
isolate.CswyAllele = CswyAllel.Allele2;
break;
case MeningoSerogroupPcr.WY:
isolate.CswyPcr = NativeMaterialTestResult.Positive;
isolate.CswyAllele = CswyAllel.Allele3;
break;
default:
throw new Exception("Unexpected Serogroup PCR for native material");
}
isolate.SerogroupPcr = MeningoSerogroupPcr.NotDetermined;
}
}
else if (Regex.Match(sending.LaboratoryNumber, "\\d+/\\d+").Success)
{
var noPrefix = sending.LaboratoryNumber.Replace("MZ", "");
var labNumberAndYear = noPrefix.Split('/');
isolate.YearlySequentialIsolateNumber = int.Parse(labNumberAndYear[0]);
isolate.Year = 2000 + int.Parse(labNumberAndYear[1]);
}
var mapping = new MeningoIsolateViewModelMappingAction();
var viewModel = new MeningoIsolateViewModel();
mapping.Process(isolate, viewModel);
var validator = new MeningoIsolateViewModelValidator();
if (validator.Validate(viewModel).Errors.Any())
{
Console.WriteLine("");
Console.WriteLine($"Validierung für Isolat {isolate.LaboratoryNumber} fehlgeschlagen:");
foreach (var error in validator.Validate(viewModel).Errors)
{
Console.WriteLine(error.ErrorMessage);
}
}
if (isolate.StemNumber.HasValue && isolate.EpsilometerTests.Any())
{
isolate.GrowthOnBloodAgar = Growth.TypicalGrowth;
isolate.GrowthOnMartinLewisAgar = Growth.TypicalGrowth;
}
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoIsolates], RESEED, {0})", isolate.MeningoSendingId - 1));
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoSendings], RESEED, {0})", isolate.MeningoSendingId - 1));
Context.MeningoIsolates.Add(isolate);
new ApplicationDbContextWrapper(Context).SaveChanges();
//Console.WriteLine(isolate);
}
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoIsolates], RESEED, {0})", currentIsolateSeed));
Context.Database.ExecuteSqlCommand(String.Format("DBCC CHECKIDENT ([MeningoSendings], RESEED, {0})", currentSendingSeed));
Console.ReadLine();
}
