public void WhenNotConfiguredFromAssembly_ReturnsNonEmptyList()
{
var sut = new MicStepsService(new NullLogger <MicStepsService>());
var steps = sut.StepsByTestingMethodAndAgent(SpeciesTestingMethod.ETest, AntifungalAgent.Caspofungin);
steps.Should().NotBeEmpty();
}
internal IEnumerable <BrothMicrodilutionStandard> Standards()
{
var standards = MicStepsService.Standards(TestingMethod).ToList();
if (!standards.Contains(Standard))
{
Standard = standards.First();
}
return(standards);
}
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");
}
internal void AddAntimicrobialSensitivityTest()
{
var antifungalAgents = MicStepsService.IsMultiAgentSystem(TestingMethod)
? MicStepsService.AntifungalAgents(TestingMethod)
: new List <AntifungalAgent> {
AntifungalAgent
};
foreach (var antifungalAgent in antifungalAgents)
{
AddAntimicrobialSensitivityTest(new AntimicrobialSensitivityTestRequest
{
TestingMethod = TestingMethod,
AntifungalAgent = antifungalAgent,
Standard = Standard
});
}
}
internal IEnumerable <AntifungalAgent> AntifungalAgents()
{
return(MicStepsService.AntifungalAgents(TestingMethod));
}
internal IEnumerable <SpeciesTestingMethod> TestingMethods()
{
return(MicStepsService.TestingMethods());
}
