public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
{
Offset = o;
ChunkData = data;
var result = BuildPerson(PersonRecords.ToList());
var person = result.Key;
if (person == null)
{
return(result.Value);
}
var observationPeriods =
BuildObservationPeriods(person.ObservationPeriodGap, ObservationPeriodsRaw.ToArray()).ToArray();
// Delete any individual that has an OBSERVATION_PERIOD that is >= 2 years prior to the YEAR_OF_BIRTH
if (Excluded(person, observationPeriods))
{
return(Attrition.ImplausibleYOBPostEarliestOP);
}
var payerPlanPeriods = BuildPayerPlanPeriods(PayerPlanPeriodsRaw.ToArray(), null).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
foreach (var visitOccurrence in BuildVisitOccurrences(VisitOccurrencesRaw.ToArray(), observationPeriods))
{
if (visitOccurrence.IdUndefined)
{
visitOccurrence.Id =
Offset.GetKeyOffset(visitOccurrence.PersonId).VisitOccurrenceId;
}
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
}
// HIX-1491 Cerner Year_of_birth should use earliest admission
if (visitOccurrences.Count > 0)
{
var minDate = visitOccurrences.Values.Min(vo => vo.StartDate);
if (person.YearOfBirth > minDate.Year)
{
person.YearOfBirth = minDate.Year;
}
}
if (person.YearOfBirth < 1900)
{
return(Attrition.ImplausibleYOBPast);
}
if (person.YearOfBirth > DateTime.Now.Year)
{
return(Attrition.ImplausibleYOBFuture);
}
var drugExposures =
BuildDrugExposures(DrugExposuresRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
var conditionOccurrences =
BuildConditionOccurrences(ConditionOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var procedureOccurrences =
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var observations = BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var measurements = BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure =
BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
// set corresponding PlanPeriodIds to drug exposure entities and procedure occurrence entities
SetPayerPlanPeriodId(payerPlanPeriods, drugExposures, procedureOccurrences,
visitOccurrences.Values.ToArray(),
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();
var visitCosts = BuildVisitCosts(visitOccurrences.Values.ToArray()).ToArray();
var devicCosts = BuildDeviceCosts(deviceExposure).ToArray();
var cohort = BuildCohort(CohortRecords.ToArray(), observationPeriods).ToArray();
var notes = BuildNote(NoteRecords.ToArray(), visitOccurrences, observationPeriods).ToArray();
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(person, death, observationPeriods, payerPlanPeriods, drugExposures,
conditionOccurrences, procedureOccurrences, observations, measurements,
visitOccurrences.Values.ToArray(), null, cohort, deviceExposure, notes);
var pg = new PregnancyAlgorithm();
foreach (var pe 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()))
{
pe.Id = Offset.GetKeyOffset(pe.PersonId).ConditionEraId;
ChunkData.ConditionEra.Add(pe);
}
return(Attrition.None);
}
/// <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);
}
public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
{
Offset = o;
ChunkData = data;
var result = BuildPerson(PersonRecords.ToList());
var buildPerson = result.Key;
if (buildPerson == null)
{
return(result.Value);
}
_currentPerson = buildPerson;
var observationPeriods =
BuildObservationPeriods(buildPerson.ObservationPeriodGap, ObservationPeriodsRaw.ToArray()).ToArray();
int age;
int.TryParse(PersonRecords.ToArray()[0].AdditionalFields["age"], out age);
_personAge = age;
int ageday;
int.TryParse(PersonRecords.ToArray()[0].AdditionalFields["ageday"], out ageday);
if (age > 0)
{
buildPerson.YearOfBirth = observationPeriods[0].StartDate.Year - age;
}
else if (string.IsNullOrEmpty(PersonRecords.ToArray()[0].AdditionalFields["ageday"]) &&
PersonRecords.ToArray()[0].AdditionalFields["age_neonate"] == "1")
{
buildPerson.YearOfBirth = observationPeriods[0].StartDate.Year;
}
else if (PersonRecords.ToArray()[0].AdditionalFields["ageday"] == null &&
PersonRecords.ToArray()[0].AdditionalFields["age_neonate"] != "1" || ageday < 0)
{
var dateOfBirth = observationPeriods[0].StartDate.AddDays(-180);
buildPerson.YearOfBirth = dateOfBirth.Year;
}
else if (ageday >= 0)
{
var dateOfBirth = observationPeriods[0].StartDate.AddDays(ageday * -1);
buildPerson.YearOfBirth = dateOfBirth.Year;
buildPerson.DayOfBirth = dateOfBirth.Day;
buildPerson.MonthOfBirth = dateOfBirth.Month;
}
if (!buildPerson.YearOfBirth.HasValue || buildPerson.YearOfBirth < 1907)
{
return(Attrition.ImplausibleYOBPast); // HIX-1417
}
// Delete any individual that has an OBSERVATION_PERIOD that is >= 2 years prior to the YEAR_OF_BIRTH
if (Excluded(buildPerson, observationPeriods))
{
return(Attrition.ImplausibleYOBPostEarliestOP);
}
var payerPlanPeriods = BuildPayerPlanPeriods(PayerPlanPeriodsRaw.ToArray(), null).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
foreach (var visitOccurrence in BuildVisitOccurrences(VisitOccurrencesRaw.ToArray(), observationPeriods))
{
if (visitOccurrence.IdUndefined)
{
visitOccurrence.Id = Offset.GetKeyOffset(visitOccurrence.PersonId).VisitOccurrenceId;
}
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
}
var drugExposures =
BuildDrugExposures(DrugExposuresRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
var conditionOccurrences =
BuildConditionOccurrences(ConditionOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var procedureOccurrences =
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var observations = BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var measurements = BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure =
BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
var death = BuildDeath(DeathRecords.ToArray(), visitOccurrences, observationPeriods);
var drugCosts = BuildDrugCosts(drugExposures).ToArray();
var procedureCosts = BuildProcedureCosts(procedureOccurrences).ToArray();
var visitCosts = BuildVisitCosts(visitOccurrences.Values.ToArray()).ToArray();
var devicCosts = BuildDeviceCosts(deviceExposure).ToArray();
foreach (var cost in visitCosts)
{
if (cost.TotalPaid == 0)
{
continue;
}
var cost52 = new Cost(cost.PersonId)
{
CostId = Offset.GetKeyOffset(cost.PersonId).VisitCostId,
CurrencyConceptId = 44818668,
TypeId = 5032,
Domain = "Visit",
EventId = cost.Id,
TotalCharge = cost.TotalPaid
};
ChunkData.AddCostData(cost52);
}
var cohort = BuildCohort(CohortRecords.ToArray(), observationPeriods).ToArray();
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(buildPerson, death, observationPeriods, payerPlanPeriods, drugExposures,
conditionOccurrences, procedureOccurrences, observations, measurements,
visitOccurrences.Values.ToArray(), null, cohort, deviceExposure, new Note[0]);
var pg = new PregnancyAlgorithm();
foreach (var pe in pg.GetPregnancyEpisodes(Vocabulary, buildPerson, observationPeriods,
ChunkData.ConditionOccurrences.Where(e => e.PersonId == buildPerson.PersonId).ToArray(),
ChunkData.ProcedureOccurrences.Where(e => e.PersonId == buildPerson.PersonId).ToArray(),
ChunkData.Observations.Where(e => e.PersonId == buildPerson.PersonId).ToArray(),
ChunkData.Measurements.Where(e => e.PersonId == buildPerson.PersonId).ToArray(),
ChunkData.DrugExposures.Where(e => e.PersonId == buildPerson.PersonId).ToArray()))
{
pe.Id = Offset.GetKeyOffset(pe.PersonId).ConditionEraId;
ChunkData.ConditionEra.Add(pe);
}
return(Attrition.None);
}
//private VisitOccurrence GetVisitOccurrence(IEntity ent)
//{
// if (_rawVisits.ContainsKey(ent.SourceRecordGuid))
// {
// var vo = _rawVisits[ent.SourceRecordGuid];
// if (vo.Id == 0 && _rawVisits.ContainsKey(vo.SourceRecordGuid) &&
// _rawVisits[vo.SourceRecordGuid].SourceRecordGuid != ent.SourceRecordGuid)
// {
// vo = _rawVisits[vo.SourceRecordGuid];
// }
// return vo;
// }
// return null;
//}
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);
}
var observationPeriods =
BuildObservationPeriods(person.ObservationPeriodGap, ObservationPeriodsRaw.ToArray()).ToArray();
// Delete any individual that has an OBSERVATION_PERIOD that is >= 2 years prior to the YEAR_OF_BIRTH
if (Excluded(person, observationPeriods))
{
return(Attrition.ImplausibleYOBPostEarliestOP);
}
var payerPlanPeriods = BuildPayerPlanPeriods(PayerPlanPeriodsRaw.ToArray(), null).ToArray();
var vDetails = BuildVisitDetails(null, VisitOccurrencesRaw.ToArray(), observationPeriods).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
var visitIds = new List <long>();
foreach (var visitOccurrence in BuildVisitOccurrences(
VisitOccurrencesRaw
.Where(v => v.AdditionalFields["sort_index"] == "1" && v.AdditionalFields["ordinal"] == "1")
.ToArray(), observationPeriods))
{
if (!_rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid))
{
_rawVisits.Add(visitOccurrence.SourceRecordGuid, visitOccurrence);
}
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
visitIds.Add(visitOccurrence.Id);
}
var visitDetails = new Dictionary <long, VisitDetail>();
foreach (var group in vDetails.GroupBy(d => d.Id))
{
var vd = group.First();
if (visitOccurrences.ContainsKey(vd.Id))
{
vd.VisitOccurrenceId = vd.Id;
vd.ProviderId = visitOccurrences[vd.Id].ProviderId;
}
else
{
var visits = visitOccurrences.Values.Where(vo =>
vo.TypeConceptId == vd.TypeConceptId && vo.StartDate >= vd.StartDate &&
vo.EndDate <= vo.EndDate).ToArray();
vd.VisitOccurrenceId = visits.Any() ? visits.First().Id : 0;
}
vd.SourceValue = $"visitid:{vd.VisitOccurrenceId};encid:{vd.AdditionalFields["encid"]}";
visitDetails.Add(vd.Id, vd);
}
long?prevVisitId = null;
foreach (var visitId in visitIds.OrderBy(v => v))
{
if (prevVisitId.HasValue)
{
visitOccurrences[visitId].PrecedingVisitOccurrenceId = prevVisitId;
}
prevVisitId = visitId;
}
UpdateVisitOccurrenceIds(visitOccurrences, visitDetails);
var drugExposures =
BuildDrugExposures(DrugExposuresRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
var conditionOccurrences =
BuildConditionOccurrences(ConditionOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var procedureOccurrences =
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var observations = BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var measurements = BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure =
BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
// set corresponding PlanPeriodIds to drug exposure entities and procedure occurrence entities
SetPayerPlanPeriodId(payerPlanPeriods, drugExposures, procedureOccurrences,
visitOccurrences.Values.ToArray(),
deviceExposure);
var notes = BuildNote(NoteRecords.ToArray(), visitOccurrences, observationPeriods).ToArray();
// set corresponding ProviderIds
SetProviderIds(drugExposures);
SetProviderIds(conditionOccurrences);
SetProviderIds(procedureOccurrences);
SetProviderIds(observations);
//SetProviderIds(visitDetails);
SetProviderIds(drugExposures, visitOccurrences);
SetProviderIds(conditionOccurrences, visitOccurrences);
SetProviderIds(measurements, visitOccurrences);
SetProviderIds(procedureOccurrences, visitOccurrences);
SetProviderIds(deviceExposure, visitOccurrences);
SetProviderIds(observations, visitOccurrences);
SetProviderIds(notes, visitOccurrences);
var death = BuildDeath(DeathRecords.ToArray(), visitOccurrences, observationPeriods);
var drugCosts = BuildDrugCosts(drugExposures).ToArray();
var procedureCosts = BuildProcedureCosts(procedureOccurrences).ToArray();
var visitCosts = BuildVisitCosts(visitOccurrences.Values.ToArray()).ToArray();
var devicCosts = BuildDeviceCosts(deviceExposure).ToArray();
var cohort = BuildCohort(CohortRecords.ToArray(), observationPeriods).ToArray();
if (death != null)
{
death = CleanUpDeath(visitOccurrences.Values, death);
death = CleanUpDeath(drugExposures, death);
death = CleanUpDeath(conditionOccurrences, death);
death = CleanUpDeath(procedureOccurrences, death);
death = CleanUpDeath(measurements, death);
death = CleanUpDeath(observations, death);
death = CleanUpDeath(deviceExposure, death);
}
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(person, death, observationPeriods, payerPlanPeriods, drugExposures,
conditionOccurrences, procedureOccurrences, observations, measurements,
visitOccurrences.Values.ToArray(), visitDetails.Values.ToArray(), cohort, deviceExposure, notes);
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);
}
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);
}
var observationPeriods =
BuildObservationPeriods(person.ObservationPeriodGap, ObservationPeriodsRaw.ToArray()).ToArray();
var payerPlanPeriods = BuildPayerPlanPeriods(PayerPlanPeriodsRaw.ToArray(), null).ToArray();
var dedupVisits = VisitOccurrencesRaw.Where(v => v.AdditionalFields["sort_index"] == "1").ToArray();
var vDetails = BuildVisitDetails(null, dedupVisits, observationPeriods).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
var visitIds = new List <long>();
foreach (var visitOccurrence in BuildVisitOccurrences(dedupVisits, observationPeriods))
{
visitOccurrence.Id = Offset.GetKeyOffset(visitOccurrence.PersonId).VisitOccurrenceId;
visitOccurrence.TypeConceptId = 44818517;
if (!visitOccurrence.EndDate.HasValue)
{
visitOccurrence.EndDate = visitOccurrence.StartDate;
}
if (!_rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid))
{
_rawVisits.Add(visitOccurrence.SourceRecordGuid, visitOccurrence);
}
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
visitIds.Add(visitOccurrence.Id);
}
var visitDetails = new Dictionary <long, VisitDetail>();
foreach (var group in vDetails.GroupBy(d => d.Id))
{
var vd = group.First();
var visitOccurrenceId = GetVisitOccurrenceId(vd);
if (visitOccurrenceId.HasValue && visitOccurrences.ContainsKey(visitOccurrenceId.Value))
{
vd.VisitOccurrenceId = visitOccurrenceId;
}
else
{
var visits = visitOccurrences.Values
.Where(vo => vd.StartDate.Date >= vo.StartDate.Date &&
vd.EndDate.Value.Date <= vo.EndDate.Value.Date).ToArray();
if (visits.Any())
{
vd.VisitOccurrenceId = visits.First().Id;
}
}
visitDetails.Add(vd.Id, vd);
}
long?prevVisitId = null;
foreach (var visitId in visitIds.OrderBy(v => v))
{
if (prevVisitId.HasValue)
{
visitOccurrences[visitId].PrecedingVisitOccurrenceId = prevVisitId;
}
prevVisitId = visitId;
}
var drugExposures =
BuildDrugExposures(DrugExposuresRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
var conditionOccurrences =
BuildConditionOccurrences(ConditionOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var procedureOccurrences =
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var observations = BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var measurements = BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure =
BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods).ToArray();
// set corresponding PlanPeriodIds to drug exposure entities and procedure occurrence entities
SetPayerPlanPeriodId(payerPlanPeriods, drugExposures, procedureOccurrences,
visitOccurrences.Values.ToArray(),
deviceExposure);
var notes = BuildNote(NoteRecords.ToArray(), visitOccurrences, observationPeriods).ToArray();
List <DateTime?> mins = new List <DateTime?>();
List <DateTime?> maxs = new List <DateTime?>();
mins.Add(GetMinDate(drugExposures));
mins.Add(GetMinDate(conditionOccurrences));
mins.Add(GetMinDate(procedureOccurrences));
mins.Add(GetMinDate(observations));
mins.Add(GetMinDate(deviceExposure));
mins.Add(GetMinDate(measurements));
mins.Add(GetMinDate(visitOccurrences.Values));
mins.Add(GetMinDate(visitDetails.Values));
maxs.Add(GetMaxDate(drugExposures));
maxs.Add(GetMaxDate(conditionOccurrences));
maxs.Add(GetMaxDate(procedureOccurrences));
maxs.Add(GetMaxDate(observations));
maxs.Add(GetMaxDate(deviceExposure));
maxs.Add(GetMaxDate(measurements));
maxs.Add(GetMaxDate(visitOccurrences.Values));
maxs.Add(GetMaxDate(visitDetails.Values));
var min = mins.Min();
var max = maxs.Max();
var observationPeriodsFinal = new List <ObservationPeriod>(1)
{
observationPeriods[0]
};
if (min.HasValue)
{
observationPeriodsFinal[0].StartDate = min.Value;
if (max.HasValue)
{
observationPeriodsFinal[0].EndDate = max;
}
else
{
observationPeriodsFinal[0].EndDate = min.Value;
}
}
// Delete any individual that has an OBSERVATION_PERIOD that is >= 2 years prior to the YEAR_OF_BIRTH
if (Excluded(person, observationPeriodsFinal))
{
return(Attrition.ImplausibleYOBPostEarliestOP);
}
// set corresponding ProviderIds
SetProviderIds(drugExposures);
SetProviderIds(conditionOccurrences);
SetProviderIds(procedureOccurrences);
SetProviderIds(observations);
SetProviderIds(deviceExposure);
SetProviderIds(measurements);
SetProviderIds(visitOccurrences.Values);
SetProviderIds(visitDetails.Values);
SetVisitOccurrenceId(conditionOccurrences, visitDetails.Values.ToArray());
SetVisitOccurrenceId(procedureOccurrences, visitDetails.Values.ToArray());
SetVisitOccurrenceId(drugExposures, visitDetails.Values.ToArray());
SetVisitOccurrenceId(deviceExposure, visitDetails.Values.ToArray());
SetVisitOccurrenceId(observations, visitDetails.Values.ToArray());
SetVisitOccurrenceId(measurements, visitDetails.Values.ToArray());
//SetVisitOccurrenceId(visitDetails.Values, visitOccurrences.Values.ToArray());
SetProviderIds(drugExposures, visitOccurrences);
SetProviderIds(conditionOccurrences, visitOccurrences);
SetProviderIds(measurements, visitOccurrences);
SetProviderIds(procedureOccurrences, visitOccurrences);
SetProviderIds(deviceExposure, visitOccurrences);
SetProviderIds(observations, visitOccurrences);
//SetProviderIds(notes, visitOccurrences); TMP: NOTE
if (notes.Any())
{
if (visitOccurrences.Count > 0)
{
foreach (var e in notes.Where(e => !e.ProviderId.HasValue))
{
if (e.AdditionalFields != null && e.AdditionalFields.ContainsKey("encid") && !string.IsNullOrEmpty(e.AdditionalFields["encid"]))
{
var encid = e.AdditionalFields["encid"];
var vd = visitDetails.Values.FirstOrDefault(v => v.AdditionalFields["encid"] == encid);
if (vd == null)
{
continue;
}
e.VisitDetailId = vd.Id;
e.VisitOccurrenceId = vd.VisitOccurrenceId;
}
if (!e.VisitOccurrenceId.HasValue)
{
continue;
}
if (visitOccurrences.ContainsKey(e.VisitOccurrenceId.Value))
{
e.ProviderId = visitOccurrences[e.VisitOccurrenceId.Value].ProviderId;
}
}
}
}
var death = BuildDeath(DeathRecords.ToArray(), visitOccurrences, observationPeriodsFinal.ToArray());
var drugCosts = BuildDrugCosts(drugExposures).ToArray();
var procedureCosts = BuildProcedureCosts(procedureOccurrences).ToArray();
var visitCosts = BuildVisitCosts(visitOccurrences.Values.ToArray()).ToArray();
var devicCosts = BuildDeviceCosts(deviceExposure).ToArray();
var cohort = BuildCohort(CohortRecords.ToArray(), observationPeriodsFinal.ToArray()).ToArray();
if (death != null)
{
death = CleanUpDeath(visitDetails.Values, death);
death = CleanUpDeath(visitOccurrences.Values, death);
death = CleanUpDeath(drugExposures, death);
death = CleanUpDeath(conditionOccurrences, death);
death = CleanUpDeath(procedureOccurrences, death);
death = CleanUpDeath(measurements, death);
death = CleanUpDeath(observations, death);
death = CleanUpDeath(deviceExposure, death);
}
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(person, death, observationPeriodsFinal.ToArray(), payerPlanPeriods, drugExposures,
conditionOccurrences, procedureOccurrences, observations, measurements,
visitOccurrences.Values.ToArray(), visitDetails.Values.ToArray(), cohort, deviceExposure, notes);
var pg = new PregnancyAlgorithm();
foreach (var r in pg.GetPregnancyEpisodes(Vocabulary, person, observationPeriodsFinal.ToArray(),
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 = Offset.GetKeyOffset(r.PersonId).ConditionEraId;
ChunkData.ConditionEra.Add(r);
}
return(Attrition.None);
}
