public void WhenCalculateResistanceBadgeWithLowerBoundaryBiggerThenSusceptibleButSusceptibleIsUnrealisticSmall_ResultIsIntermediate()
{
var component = CreateSut();
var sut = component.Instance;
var breakPoint = new MockClinicalBreakpointService.MockClinicalBreakPoint()
{
AntifungalAgent = AntifungalAgent.Flucytosine,
MicBreakpointSusceptible = 0.001f,
MicBreakpointResistent = 100f,
Species = Species.CandidaParapsilosis,
};
_mockClinicalBreakpointService.AddBreakpoint(100000, breakPoint);
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
ClinicalBreakpointId = 100000,
AntifungalAgent = AntifungalAgent.Flucytosine,
MinimumInhibitoryConcentration = _mockMicStepsService.StepsByTestingMethodAndAgent(SpeciesTestingMethod.Vitek, AntifungalAgent.Flucytosine).First().Value
};
sut.SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
var badge = sut.ResistanceBadge(sensitivityTest);
badge.Should().Be("bg-warning");
sensitivityTest.Resistance.Should().Be(Resistance.Intermediate);
}
internal string DuplicateClass(AntimicrobialSensitivityTestRequest sensitivityTest)
{
var isDuplicate = SentinelEntry.AntimicrobialSensitivityTests.Count(
s => s.AntifungalAgent == sensitivityTest.AntifungalAgent &&
s.Standard == sensitivityTest.Standard &&
s.TestingMethod == sensitivityTest.TestingMethod) > 1;
return(isDuplicate ? "duplicate-sensitivity-test" : "");
}
internal IEnumerable <MicStep> MicSteps(AntimicrobialSensitivityTestRequest sensitivityTest)
{
var matchingSteps = MicStepsService.StepsByTestingMethodAndAgent(sensitivityTest.TestingMethod, sensitivityTest.AntifungalAgent);
if (sensitivityTest.MinimumInhibitoryConcentration.HasValue && matchingSteps.Any() && matchingSteps.All(s => !s.Value.Equals(sensitivityTest.MinimumInhibitoryConcentration)))
{
sensitivityTest.MinimumInhibitoryConcentration = matchingSteps.First().Value;
}
return(matchingSteps);
}
//TODO move resistance evaluation to a pure business logic class
internal string ResistanceBadge(AntimicrobialSensitivityTestRequest sensitivityTest)
{
Logger.LogInformation("Resistance update");
var breakpoint = AllBreakpoints.FirstOrDefault(b => b.Id == sensitivityTest.ClinicalBreakpointId);
if (breakpoint?.MicBreakpointResistent == null || !breakpoint.MicBreakpointSusceptible.HasValue)
{
if (breakpoint == null)
{
Logger.LogWarning($"No breakpoint found for {sensitivityTest.TestingMethod}/{sensitivityTest.AntifungalAgent} where id is {sensitivityTest.ClinicalBreakpointId}");
}
else
{
Logger.LogInformation($"Breakpoints {breakpoint.Id} (resistant/susceptible) values are not complete ({breakpoint.MicBreakpointResistent}/{breakpoint.MicBreakpointSusceptible})");
}
sensitivityTest.Resistance = Resistance.NotDetermined;
return("bg-info");
}
var selectedStep = MicStepsService.StepsByTestingMethodAndAgent(sensitivityTest.TestingMethod, sensitivityTest.AntifungalAgent)
.FirstOrDefault(s => s.Value.Equals(sensitivityTest.MinimumInhibitoryConcentration));
if (selectedStep != null && Math.Abs(breakpoint.MicBreakpointSusceptible.Value - EucastExtraLowSusceptibleValueToAlwaysGetIntermediate) > 0.001f)
{
if (selectedStep.LowerBoundary && sensitivityTest.MinimumInhibitoryConcentration > breakpoint.MicBreakpointSusceptible ||
selectedStep.UpperBoundary && sensitivityTest.MinimumInhibitoryConcentration < breakpoint.MicBreakpointResistent)
{
sensitivityTest.Resistance = Resistance.NotEvaluable;
return("bg-info");
}
}
Logger.LogInformation($"Found breakpoint for {sensitivityTest.TestingMethod}/{sensitivityTest.AntifungalAgent} where id is {sensitivityTest.ClinicalBreakpointId}: {breakpoint.Title}");
var mic = sensitivityTest.MinimumInhibitoryConcentration;
if (IsResistantAccordingToEucastDefinition(mic, breakpoint))
{
sensitivityTest.Resistance = Resistance.Resistant;
return("bg-danger");
}
if (IsResistantAccordingToClsiDefinition(mic, breakpoint))
{
sensitivityTest.Resistance = Resistance.Resistant;
return("bg-danger");
}
if (IsSusceptibleAccordingToBothDefinitions(mic, breakpoint))
{
sensitivityTest.Resistance = Resistance.Susceptible;
return("bg-success");
}
sensitivityTest.Resistance = Resistance.Intermediate;
return("bg-warning");
}
public void WhenCalculateResistanceBadgeWhereBreakpointHasNoMics_ResultsInNotDetermined()
{
var component = CreateSut();
var sut = component.Instance;
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
ClinicalBreakpointId = 1234567,
MinimumInhibitoryConcentration = 0.25f
};
sut.SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
var badge = sut.ResistanceBadge(sensitivityTest);
badge.Should().Be("bg-info");
sensitivityTest.Resistance.Should().Be(Resistance.NotDetermined);
}
public void WhenNoApplicableBreakpoint_SensitivityIsSetToNotDetermined()
{
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
AntifungalAgent = AntifungalAgent.Fluorouracil,
Standard = BrothMicrodilutionStandard.Eucast,
Resistance = Resistance.Susceptible
};
var component = CreateSut();
var sut = component.Instance;
sut.SentinelEntry.IdentifiedSpecies = Species.CandidaTropicalis;
sut.ApplicableBreakpoints(sensitivityTest);
sensitivityTest.Resistance.Should().Be(Resistance.NotDetermined);
}
public void WhenApplicableBreakpoints_OnlyValidOnesAreReturned()
{
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
AntifungalAgent = AntifungalAgent.Micafungin,
Standard = BrothMicrodilutionStandard.Eucast
};
var component = CreateSut();
var sut = component.Instance;
sut.SentinelEntry.IdentifiedSpecies = Species.CandidaAlbicans;
var breakpoints = sut.ApplicableBreakpoints(sensitivityTest).ToList();
breakpoints.Should().HaveCount(1);
breakpoints.Should().OnlyContain(
b => b.AntifungalAgent == AntifungalAgent.Micafungin && b.Standard == BrothMicrodilutionStandard.Eucast);
}
public void WhenCalculateResistanceBadgeWithNoMatchingBreakpoint_ResultsInNotDetermined()
{
var component = CreateSut();
var sut = component.Instance;
sut.SentinelEntry.IdentifiedSpecies = Species.CandidaAlbicans;
var firstBreakpoint = sut.AllBreakpoints.First(b =>
!b.MicBreakpointResistent.HasValue && !b.MicBreakpointSusceptible.HasValue);
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
ClinicalBreakpointId = firstBreakpoint.Id,
MinimumInhibitoryConcentration = 0.25f
};
sut.SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
var badge = sut.ResistanceBadge(sensitivityTest);
badge.Should().Be("bg-info");
sensitivityTest.Resistance.Should().Be(Resistance.NotDetermined);
}
internal IEnumerable <ClinicalBreakpoint> ApplicableBreakpoints(AntimicrobialSensitivityTestRequest sensitivityTest)
{
var antifungalAgent = sensitivityTest.AntifungalAgent;
var applicableBreakpoints = AllBreakpoints.Where(b =>
b.AntifungalAgent == antifungalAgent &&
b.Species == SentinelEntry.IdentifiedSpecies &&
b.Standard == sensitivityTest.Standard).ToList();
if (applicableBreakpoints.All(b => b.Id != sensitivityTest.ClinicalBreakpointId))
{
Logger.LogInformation($"Update test {sensitivityTest.AntifungalAgent} to breakpoint id {applicableBreakpoints.FirstOrDefault()?.Id}");
sensitivityTest.ClinicalBreakpointId = applicableBreakpoints.FirstOrDefault()?.Id;
}
Logger.LogInformation($"Found {applicableBreakpoints.Count} applicable breakpoints for {antifungalAgent} and {SentinelEntry.IdentifiedSpecies}");
if (!applicableBreakpoints.Any())
{
sensitivityTest.Resistance = Resistance.NotDetermined;
}
return(applicableBreakpoints);
}
public void WhenCalculateResistanceBadge_UsesBreakpointValuesWithClsiBoundaryConditions(float deltaToResistance, string expectedBadge, Resistance expectedResistance)
{
var component = CreateSut();
var sut = component.Instance;
sut.SentinelEntry.IdentifiedSpecies = Species.CandidaGlabrata;
var breakpoint = sut.AllBreakpoints.Single(b =>
b.AntifungalAgent == AntifungalAgent.Caspofungin &&
b.Species == Species.CandidaGlabrata &&
b.Standard == BrothMicrodilutionStandard.Clsi &&
b.Version == "M60 2019");
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
ClinicalBreakpointId = breakpoint.Id,
MinimumInhibitoryConcentration = breakpoint.MicBreakpointResistent.Value + deltaToResistance
};
sut.SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
var badge = sut.ResistanceBadge(sensitivityTest);
badge.Should().Be(expectedBadge);
sensitivityTest.Resistance.Should().Be(expectedResistance);
}
public void WhenCalculateResistanceBadge_UsesBreakpointValuesWithEucastBoundaryConditions(float deltaToResistance, string expectedBadge, Resistance expectedResistance)
{
var component = CreateSut();
var sut = component.Instance;
sut.SentinelEntry.IdentifiedSpecies = Species.CandidaAlbicans;
var firstBreakpoint = sut.AllBreakpoints.Single(b =>
b.AntifungalAgent == AntifungalAgent.Voriconazole &&
b.Species == Species.CandidaDubliniensis &&
b.Standard == BrothMicrodilutionStandard.Eucast &&
b.Version == "10.0");
var sensitivityTest = new AntimicrobialSensitivityTestRequest
{
ClinicalBreakpointId = firstBreakpoint.Id,
MinimumInhibitoryConcentration = firstBreakpoint.MicBreakpointResistent.Value + deltaToResistance
};
sut.SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
var badge = sut.ResistanceBadge(sensitivityTest);
badge.Should().Be(expectedBadge);
sensitivityTest.Resistance.Should().Be(expectedResistance);
}
internal void RemoveAntimicrobialSensitivityTest(AntimicrobialSensitivityTestRequest sensitivityTest)
{
SentinelEntry.AntimicrobialSensitivityTests.Remove(sensitivityTest);
}
private void AddAntimicrobialSensitivityTest(AntimicrobialSensitivityTestRequest sensitivityTest)
{
SentinelEntry.AntimicrobialSensitivityTests.Add(sensitivityTest);
sensitivityTest.ClinicalBreakpointId = ApplicableBreakpoints(sensitivityTest).FirstOrDefault()?.Id;
}