public async Task <IActionResult> UpdateOutbreak([FromBody] UpdateOutbreak command)
{
await rules
.RequireSettingInformation()
.RequireDocumentsWhenAfterActionReportCompleted()
.RequireModeOfTransmission()
.RequireHumanSpecimenConfirmation()
.Apply(command, ModelState);
if (!ModelState.IsValid)
{
return(BadRequest(ModelState));
}
await service.Execute(command);
return(Ok());
}
private async Task SaveOutbreak(UpdateOutbreak command)
{
var outbreak = await writeContext.Outbreak
.Include(ob => ob.OutbreakEvents)
.Include(ob => ob.OutbreakSymptoms)
.FirstAsync(ob => ob.IdOutbreak == command.OutbreakId);
using (var transaction = writeContext.Database.BeginTransaction())
{
//calculate the event date
outbreak.DtOutbreakEvent = new DateTime?[]
{
outbreak.DtEarliestOnset,
outbreak.DtEarliestExposure,
outbreak.DtChdNotified,
outbreak.DtOutbreakEvent
}
.Where(d => d.HasValue)
.OrderBy(d => d)
.First();
//so all events have the same timestamp
var eventDate = DateTime.Now;
await ReplaceEvents(outbreak, OutbreakEventType.Investigation, command.InvestigationMethods, eventDate, CodeType.OutbreakInvestigation);
await ReplaceEvents(outbreak, OutbreakEventType.StudyDesign, command.StudyDesigns, eventDate, CodeType.OutbreakStudyDesign);
await ReplaceEvents(outbreak, OutbreakEventType.MultiCounty, command.OtherCountiesList, eventDate, CodeType.County);
await ReplaceEvents(outbreak, OutbreakEventType.MultiCountry, command.OtherCountriesList, eventDate, CodeType.Country, CodeType.Region);
await ReplaceEvents(outbreak, OutbreakEventType.MultiState, command.OtherStatesList, eventDate, CodeType.State);
await ReplaceEvents(outbreak, OutbreakEventType.Regulatory, command.RegulatoryAgencies, eventDate, CodeType.OutbreakRegulatory);
await CreateEvent(outbreak, OutbreakEventType.CaseDefinition, command.CaseDefinition, eventDate);
await CreateEvent(outbreak, OutbreakEventType.LabFindings, command.LabFindings, eventDate);
await CreateEvent(outbreak, OutbreakEventType.Closure, command.Decisions, eventDate, OutbreakEventType.ConclusionNotes);
await CreateEvent(outbreak, OutbreakEventType.Closure, command.Recommendations, eventDate, OutbreakEventType.Recommendations);
await CreateEvent(outbreak, OutbreakEventType.ProcessImprovements, command.ImprovementAreas, eventDate);
await CreateEvent(outbreak, OutbreakEventType.EpiComPostId, command.PostId.ToString(), eventDate);
ReplaceSymptoms(outbreak, command.Symptom, command.OtherSymptom);
outbreak.NmOutbreak = command.EventName;
//if ICD9 changes update all associated cases
if (outbreak.CdIcd9 != command.DiseaseHazard)
{
string sql = "update dbo.epi_case set CD_ICD9 = @icd9 where id_outbreak = @outbreakId";
var connection = writeContext.Database.GetDbConnection().EnsureOpen();
await connection.ExecuteAsync(sql, new
{
icd9 = command.DiseaseHazard,
outbreakId = command.OutbreakId
}, transaction.GetDbTransaction());
outbreak.CdIcd9 = command.DiseaseHazard;
//only need to ensure a survey is created/exists when ICD9 changes
await EnsureOutbreakSurvey(outbreak);
}
outbreak.CdCountyInitiating = command.County;
outbreak.InMultiCounty = command.OtherCountiesAffected;
outbreak.InMultiState = command.OtherStatesAffected;
outbreak.DsStateConsulted = command.StaffConsulted;
outbreak.NmInvestigator = command.Investigator;
outbreak.CdModeTransmission = command.TransmissionMode;
outbreak.InFoodWater = command.FoodOrWaterRelated;
outbreak.InVehicleFw = command.IsVehicleIdentified;
outbreak.DsVehicleFw = command.Vehicle;
outbreak.InHealthcare = command.HealthRelated;
outbreak.CdVehicleIdentified = command.CauseForOutbreak;
outbreak.DsVehicleHai = command.Description;
outbreak.CdModeTransmission = command.TransmissionMode;
outbreak.InFoodWater = command.FoodOrWaterRelated;
outbreak.InVehicleFw = command.IsVehicleIdentified;
outbreak.DsVehicleFw = command.Vehicle;
outbreak.InHealthcare = command.HealthRelated;
outbreak.CdVehicleIdentified = command.CauseForOutbreak;
outbreak.DsVehicleHai = command.Description;
outbreak.CdErDeptVisitsType = command.EmergencyVisitsType;
outbreak.AmErDeptVisits = command.EmergencyVisits;
outbreak.CdInpatientHosptialType = command.InpatientHospitalizationsType;
outbreak.AmInpatientHospital = command.InpatientHospitalizations;
outbreak.AmDeaths = command.Deaths;
outbreak.CdDeathsType = command.DeathsType;
outbreak.DtChdNotified = command.NotifiedDate;
outbreak.CdReporterType = command.FirstNotified;
outbreak.NmReporter = command.ReporterName ?? string.Empty;
outbreak.DtInvestigated = command.InvestigationStarted;
outbreak.DtClosed = command.InvestigationClosed;
outbreak.CdStatus = outbreak.DtClosed != null ? "CLOSED" : "OPEN";
outbreak.CdSyndromes = command.Syndrome;
outbreak.DsSyndromeOther = command.OtherSyndrome;
outbreak.DsDiseaseHazardOther = command.OtherDiseaseHazard;
outbreak.AmEstimatedIll = command.EstimatedNumber.GetValueOrDefault();
outbreak.InInvestigated = command.IsInvestigated;
outbreak.InOutbreak = command.IsOutbreak;
outbreak.InRecommendations = command.IsRecProvided;
outbreak.CdRecommendationsHow = command.MethodofRec;
//TODO: this does not look correct
outbreak.InImplemented = command.WereRecommendationsImplemented;
outbreak.InInternalAction = command.IsReportCompleted;
outbreak.DtEarliestExposure = command.FirstExposureDate;
outbreak.DtLastExposure = command.LastExposureDate;
outbreak.DtEarliestOnset = command.FirstOnsetDate;
outbreak.DtLastOnset = command.LastOnsetDate;
outbreak.AmMedianDuration = command.Duration;
outbreak.CdMedianDurationUnit = command.TimeUnit;
outbreak.InLabConfirmed = command.IsHumanSpecimens;
outbreak.InLabConducted = command.IsLabTestingConducted;
outbreak.AmLabConfirmed = (short?)command.NoOfCases;
//TODO: verify this does not look correct
outbreak.InLabConfirmedFood = command.IsFoodSpecimens;
outbreak.AmTotalCases = command.TotalCases;
outbreak.CdTotalCaseType = command.TotalCaseType;
outbreak.AmNonStaffCases = command.NonStaffCases;
outbreak.AmStaffCases = command.StaffCases;
outbreak.AmUnknownCases = command.UnknownCases;
if (!string.IsNullOrWhiteSpace(command.Comments))
{
await CreateEvent(outbreak, OutbreakEventType.Review, command.Comments, eventDate);
}
if (outbreak.CdReviewStatus != command.ReviewStatus)
{
outbreak.IdReviewer = usernameProvider.GetUsername();
outbreak.DtReview = DateTime.Now;
outbreak.CdReviewStatus = command.ReviewStatus;
}
await writeContext.SaveChangesAsync();
transaction.Commit();
}
//save survey
//NOTE: This is not transacted with outbreak save
//if can be, but it requires detecting a current pending transaction inside survey answer save
if (command.SurveyUid != null)
{
await surveyService.Execute(new SaveSurveyAnswers
{
OutbreakId = outbreak.IdOutbreak,
Answers = command.SurveyAnswers,
SurveyId = command.SurveyUid.Value
});
}
}
public async Task Execute(UpdateOutbreak command)
{
await SaveOutbreak(command);
///**********Results****************/
//outbreak.AmTotalCases = command.Results.TotalCaseResults.TotalCases;
//outbreak.AmTotalExposed = command.Results.TotalCaseResults.TotalExposed;
//outbreak.AmMale = command.Results.GenderResults.MaleCases;
//outbreak.AmFemale = command.Results.GenderResults.FemaleCases;
//outbreak.AmGenderUnknown = command.Results.GenderResults.UnknownGenderCases;
//outbreak.AmStaffCases = command.Results.StaffExposureResults.StaffCases;
//outbreak.AmStaffExposed = command.Results.StaffExposureResults.StaffExposed;
//outbreak.AmNonStaffCases = command.Results.StaffExposureResults.NonstaffCases;
//outbreak.AmNonStaffExposed = command.Results.StaffExposureResults.NonstaffExposed;
//outbreak.AmUnknownCases = command.Results.StaffExposureResults.UnknownCases;
//outbreak.AmUnknownExposed = command.Results.StaffExposureResults.UnknownExposed;
//outbreak.AmAgeLess1 = command.Results.AgeResults.AgeLessthan1;
//outbreak.AmAge14 = command.Results.AgeResults.Age1to4;
//outbreak.AmAge59 = command.Results.AgeResults.Age5to9;
//outbreak.AmAge1019 = command.Results.AgeResults.Age10to19;
//outbreak.AmAge2049 = command.Results.AgeResults.Age20to49;
//outbreak.AmAge5074 = command.Results.AgeResults.Age50to74;
//outbreak.AmAgeGreater74 = command.Results.AgeResults.AgeGreater74;
//outbreak.AmAgeUnknown = command.Results.AgeResults.AgeUnknown;
//outbreak.AmWithInfoSought = command.Results.OutComeResults.InfoAvailable;
//outbreak.AmSoughtHealthcare = command.Results.OutComeResults.SoughtCases;
//outbreak.AmErVisit = command.Results.OutComeResults.ErCases;
//outbreak.AmHospitalization = command.Results.OutComeResults.InpatientCases;
//outbreak.AmDied = command.Results.OutComeResults.DiedCases;
//outbreak.AmWithInfoSought = command.Results.OutComeResults.SoughtCasesWithInfo;
//outbreak.AmWithInfoErVisit = command.Results.OutComeResults.ErCasesWithInfo;
//outbreak.AmWithInfoHospitalization = command.Results.OutComeResults.InpatientCasesWithInfo;
//outbreak.AmWithInfoDied = command.Results.OutComeResults.DiedCasesWithInfo;
///**********Clinical results****************/
//var firstOnsetDateOrMaxValue = String.IsNullOrEmpty(command.ClinicalResults.FirstOnsetDate) ? DateTime.MaxValue : Convert.ToDateTime(command.ClinicalResults.FirstOnsetDate);
//var firstExposureDateOrMaxValue = String.IsNullOrEmpty(command.ClinicalResults.FirstExposureDate) ? DateTime.MaxValue : Convert.ToDateTime(command.ClinicalResults.FirstExposureDate);
//var notifiedDate = Convert.ToDateTime(command.Background.NotifiedDate);
//var minDate = new DateTime(Math.Min(((DateTime)firstExposureDateOrMaxValue).Ticks, (new DateTime(Math.Min(((DateTime)firstOnsetDateOrMaxValue).Ticks, ((DateTime)notifiedDate).Ticks))).Ticks));
//bool noOutbreakLevelSurveyExists = !writeContext.Survey
// .Any(survey => survey.CdSurveyType == "OUTBREAK_LEVEL"
// && survey.IdOutbreak.Equals(command.OutbreakId)
// && (survey.IdSurveyVersion == 1));
//bool diseaseCodeExists = !String.IsNullOrEmpty(command.Background.DiseaseHazard);
//if (noOutbreakLevelSurveyExists && diseaseCodeExists)
//{
// var existingOutbreakTemplateSurvey = await writeContext.Survey
// .Where(survey => survey.CdSurveyType.Equals("OUTBREAK_TEMPLATE")
// && survey.CdIcd9.Equals(command.Background.DiseaseHazard)
// && (survey.DtEffective <= minDate)
// && (survey.IdSurveyVersion == 1))
// .FirstOrDefaultAsync();
// if (existingOutbreakTemplateSurvey != null)
// {
// var newSurveyId = (int)await sequenceGenerator.GetNextAsync(SequenceType.Survey);
// Merlin.Core.Data.Survey newSurvey = new Merlin.Core.Data.Survey
// {
// IdSurvey = newSurveyId,
// NmSurvey = existingOutbreakTemplateSurvey.NmSurvey + " " + command.Background.EventName,
// IdOutbreak = command.OutbreakId,
// DtEffective = minDate,
// IdAdded = command.IdUser,
// DtAdded = DateTime.Now,
// UidLayout = existingOutbreakTemplateSurvey.UidLayout,
// CdSurveyType = "OUTBREAK_LEVEL",
// IdSurveyVersion = 1,
// UID = Guid.NewGuid()
// };
// writeContext.Survey.Add(newSurvey);
// }
//}
///**********EpiCom****************/
////EpiCom post submitted separately
//if (command.Epicom.PostId.HasValue)
//{
// var currentPostId = await writeContext.OutbreakEvents
// .Where(x => x.CdEventType.Equals("EPICOM_POST_ID") && x.IdOutbreak == command.OutbreakId)
// .OrderByDescending(x => x.IdEvent)
// .Select(x => x.DsDesc)
// .FirstOrDefaultAsync();
// if (!command.Epicom.PostId.Equals(currentPostId))
// {
// EventId = (int)await sequenceGenerator.GetNextAsync(SequenceType.OutbreakEventId);
// OutbreakEvents newEvent = new OutbreakEvents
// {
// IdOutbreak = command.OutbreakId,
// CdEventType = "EPICOM_POST_ID",
// IdEvent = EventId,
// CdSubType = "",
// DsDesc = command.Epicom.PostId.ToString(),
// IdSequence = 0,
// IdAdded = command.Epicom.Author
// };
// writeContext.OutbreakEvents.Add(newEvent);
// }
//}
}
