public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
{
Offset = o;
ChunkData = data;
//"If the claim is associated with a diagnosis, " +
//"and (1) that [Diagnosis].[Month and year of start of medical care] date falls within the [Month and year of medical care] and (2) " +
//"there is no other diagnoses with the same level 4 ICD-10 code from the same institution for the same member with the same [Month and year of start of medical care] date, " +
//"then the [Month and year of start of medical care] date is used as the visit_start_date."
foreach (var sameSource in ConditionOccurrencesRaw
.Where(c => !string.IsNullOrEmpty(c.AdditionalFields["start_m_and_y_date"]))
.GroupBy(c => c.SourceValue))
{
foreach (var sameInstitution in sameSource.GroupBy(c => c.ProviderId))
{
foreach (var sameStartOfMedicalCare in sameInstitution.GroupBy(c =>
c.AdditionalFields["month_and_year_of_start"]))
{
var diagnosis = sameStartOfMedicalCare.ToList();
if (diagnosis.Count == 1)
{
if (!_visitsDateDiagnosis.ContainsKey(diagnosis[0].VisitOccurrenceId.Value))
{
_visitsDateDiagnosis.Add(diagnosis[0].VisitOccurrenceId.Value,
DateTime.Parse(diagnosis[0].AdditionalFields["start_m_and_y_date"]));
}
else
{
var newValue = DateTime.Parse(diagnosis[0].AdditionalFields["start_m_and_y_date"]);
if (_visitsDateDiagnosis[diagnosis[0].VisitOccurrenceId.Value] < newValue)
{
_visitsDateDiagnosis[diagnosis[0].VisitOccurrenceId.Value] = newValue;
}
}
}
}
}
}
//If the claim is associated with a Drug.[Prescription date] or Procedure.[Procedure date], use the minimum of those dates as the visit_start_date.
foreach (var p in ProcedureOccurrencesRaw.GroupBy(p => p.VisitOccurrenceId))
{
var procedure = p.First();
if (!procedure.VisitOccurrenceId.HasValue)
{
continue;
}
var procedures = p.Where(pp => pp.StartDate > DateTime.MinValue).ToArray();
if (procedures.Length > 0)
{
var minProcedureDate = procedures.Min(pp => pp.StartDate);
if (_visitsDate.ContainsKey(procedure.VisitOccurrenceId.Value))
{
_visitsDate[procedure.VisitOccurrenceId.Value] = minProcedureDate;
continue;
}
_visitsDate.Add(procedure.VisitOccurrenceId.Value, minProcedureDate);
}
}
foreach (var d in DrugExposuresRaw.GroupBy(d => d.VisitOccurrenceId))
{
var drug = d.First();
if (!drug.VisitOccurrenceId.HasValue)
{
continue;
}
var drugs = d.Where(dd => dd.StartDate > DateTime.MinValue).ToArray();
if (drugs.Length > 0)
{
var minDrugDate = drugs.Min(dd => dd.StartDate);
if (!_visitsDate.ContainsKey(drug.VisitOccurrenceId.Value))
{
_visitsDate.Add(drug.VisitOccurrenceId.Value, minDrugDate);
continue;
}
// [Date of prescription] < [Date of procedure]
// minDrugDate < visitsDate[drug.VisitOccurrenceId.Value]
if (minDrugDate < _visitsDate[drug.VisitOccurrenceId.Value])
{
_visitsDate[drug.VisitOccurrenceId.Value] = minDrugDate;
}
}
}
return(base.Build(data, o));
}
/// <summary>
/// Build person entity and all person related entities like: DrugExposures, ConditionOccurrences, ProcedureOccurrences... from raw data sets
/// </summary>
public override Attrition Build(ChunkData data, KeyMasterOffsetManager om)
{
this.Offset = om;
this.ChunkData = data;
var result = BuildPerson(PersonRecords.ToList());
var person = result.Key;
if (person == null)
{
return(result.Value);
}
if (!ObservationPeriodsRaw.Any(op => op.StartDate < op.EndDate))
{
return(Attrition.InvalidObservationTime);
}
var observationPeriods =
BuildObservationPeriods(person.ObservationPeriodGap,
ObservationPeriodsRaw.Where(op => op.StartDate < op.EndDate).ToArray()).ToArray();
var payerPlanPeriods = BuildPayerPlanPeriods(PayerPlanPeriodsRaw.ToArray(), null).ToArray();
var cohort = BuildCohort(CohortRecords.ToArray(), observationPeriods).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
var visitIds = new List <long>();
// Build and clenaup visit occurrences entities
foreach (var visitOccurrence in CleanupVisits(
BuildVisitOccurrences(VisitOccurrencesRaw.ToArray(), observationPeriods), cohort,
observationPeriods))
{
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
visitIds.Add(visitOccurrence.Id);
}
long?prevVisitId = null;
foreach (var visitId in visitIds.OrderBy(v => v))
{
if (prevVisitId.HasValue)
{
visitOccurrences[visitId].PrecedingVisitOccurrenceId = prevVisitId;
}
prevVisitId = visitId;
}
var drugExposures = BuildDrugExposures(DrugExposuresRaw.Where(de => de.StartDate < DateTime.Now).ToArray(),
visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure = BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var conditionOccurrences =
Cleanup(
BuildConditionOccurrences(
ConditionOccurrencesRaw.Where(co => co.StartDate < DateTime.Now).ToArray(), visitOccurrences,
observationPeriods),
cohort).ToArray();
var procedureOccurrences =
Cleanup(
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods),
cohort).ToArray();
var observations =
Cleanup(BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods), cohort)
.ToArray();
var measurements =
Cleanup(BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods), cohort)
.ToArray();
// set corresponding PlanPeriodIds to drug exposure entities and procedure occurrence entities
SetPayerPlanPeriodId(payerPlanPeriods, drugExposures, procedureOccurrences,
visitOccurrences.Values.ToArray(), new DeviceExposure[] { });
// set corresponding ProviderIds
SetProviderIds(drugExposures);
SetProviderIds(conditionOccurrences);
SetProviderIds(procedureOccurrences);
SetProviderIds(observations);
var death = BuildDeath(DeathRecords.ToArray(), visitOccurrences, observationPeriods);
var drugCosts = BuildDrugCosts(drugExposures).ToArray();
var procedureCosts = BuildProcedureCosts(procedureOccurrences).ToArray();
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(person, death,
observationPeriods,
payerPlanPeriods,
drugExposures,
CleanupCondition(conditionOccurrences).ToArray(),
procedureOccurrences,
CleanupObservations(observations, measurements, conditionOccurrences, procedureOccurrences).ToArray(),
measurements,
visitOccurrences.Values.ToArray(), null, cohort, deviceExposure, new Note[0]);
var pg = new PregnancyAlgorithm.PregnancyAlgorithm();
foreach (var r in pg.GetPregnancyEpisodes(Vocabulary, person, observationPeriods,
ChunkData.ConditionOccurrences.Where(e => e.PersonId == person.PersonId).ToArray(),
ChunkData.ProcedureOccurrences.Where(e => e.PersonId == person.PersonId).ToArray(),
ChunkData.Observations.Where(e => e.PersonId == person.PersonId).ToArray(),
ChunkData.Measurements.Where(e => e.PersonId == person.PersonId).ToArray(),
ChunkData.DrugExposures.Where(e => e.PersonId == person.PersonId).ToArray()))
{
r.Id = KeyMasterOffsetManager.GetKeyOffset(r.PersonId).ConditionEraId;
ChunkData.ConditionEra.Add(r);
}
return(Attrition.None);
}