private bool AddCost(long eventId, Func <ICostV5, Cost> createCost, IEntity entity, ICostV5 entityCost)
{
if (entityCost == null)
{
return(false);
}
var cost = createCost(entityCost);
cost.CostId = Offset.GetKeyOffset(entityCost.PersonId).VisitCostId;
cost.EventId = eventId;
return(ChunkData.AddCostData(cost));
}
public IEnumerable <Note> GetNotes(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
return
(base.GetConcepts(concept, reader, offset)
.Select(
e =>
new Note
{
Id = offset.GetKeyOffset(e.PersonId).NoteId,
EncodingConceptId = reader.GetInt(EncodingConceptId) ?? 0,
LanguageConceptId = reader.GetInt(LanguageConceptId) ?? 0,
Title = reader.GetString(Title),
Text = reader.GetString(Text),
PersonId = e.PersonId,
ConceptId = e.ConceptId,
StartDate = e.StartDate,
TypeConceptId = e.TypeConceptId,
VisitOccurrenceId = e.VisitOccurrenceId,
VisitDetailId = e.VisitDetailId,
SourceValue = e.SourceValue,
ProviderId = e.ProviderId,
AdditionalFields = e.AdditionalFields
}));
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
int?relevantConditionConceptId = null;
int?modifierConceptId = reader.GetInt(ModifierConceptId) ?? 0;
if (Concepts.Length == 2)
{
var relevantConcepts = Concepts[1].GetConceptIdValues(Vocabulary, Concepts[1].Fields[0], reader);
if (relevantConcepts.Count > 0)
{
relevantConditionConceptId = relevantConcepts.Min(c => c.ConceptId); //CDM v4
modifierConceptId = relevantConditionConceptId; //CDM v5
}
}
foreach (var e in base.GetConcepts(concept, reader, offset))
{
yield return
(new ProcedureOccurrence(e)
{
Id = KeyMasterOffsetManager.GetKeyOffset(e.PersonId).ProcedureOccurrenceId,
ReleventConditionConceptId = relevantConditionConceptId,
ModifierConceptId = modifierConceptId ?? 0,
StartTime = e.StartTime ?? e.StartDate.ToString("HH:mm:ss", CultureInfo.InvariantCulture),
Quantity = reader.GetInt(Quantity),
QualifierSourceValue = reader.GetString(QualifierSourceValue)
});
}
}
public object GetValue(int i)
{
if (_enumerator.Current == null)
{
return(null);
}
switch (i)
{
case 0:
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.TypeConceptId);
case 5:
return(_enumerator.Current.ModifierConceptId);
case 6:
return(_enumerator.Current.Quantity);
case 7:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 8:
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (KeyMasterOffsetManager.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
case 9:
return(_enumerator.Current.SourceValue);
case 10:
return(_enumerator.Current.SourceConceptId);
case 11:
return(_enumerator.Current.QualifierSourceValue);
default:
throw new NotImplementedException();
}
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
return(_offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.EndDate);
case 5:
return(_enumerator.Current.TypeConceptId);
case 6:
return(_enumerator.Current.StopReason);
case 7:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 8:
{
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
}
case 9:
return(_enumerator.Current.StatusConceptId);
case 10:
return(_enumerator.Current.SourceValue);
case 11:
return(_enumerator.Current.SourceConceptId);
case 12:
return(_enumerator.Current.StatusSourceValue);
default:
throw new NotImplementedException();
}
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.StartDate);
case 3:
return(_enumerator.Current.StartTime);
case 4:
return(_enumerator.Current.TypeConceptId);
case 5:
return(_enumerator.Current.Text);
case 6:
return(_enumerator.Current.ProviderId);
case 7:
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (KeyMasterOffsetManager.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
case 8:
return(_enumerator.Current.SourceValue);
case 9:
return(_enumerator.Current.ConceptId);
case 10:
return(_enumerator.Current.Title);
case 11:
return(_enumerator.Current.EncodingConceptId);
case 12:
return(_enumerator.Current.LanguageConceptId);
default:
throw new NotImplementedException();
}
}
public static List <PayerPlanPeriod> GetPayerPlanPeriods(PayerPlanPeriod[] entities, int gap, Func <PayerPlanPeriod, PayerPlanPeriod, bool> canBeCombined, KeyMasterOffsetManager offset)
{
var result = new List <PayerPlanPeriod>();
if (entities.Length == 0)
{
return(result);
}
var ordered =
entities.OrderBy(e => e.StartDate).ToList();
var payerPlanPeriod = ordered[0];
var list = new List <PayerPlanPeriod>();
foreach (var entity in ordered)
{
if (canBeCombined(entity, payerPlanPeriod))
{
list.Add(entity);
continue;
}
result.AddRange(GetEras(list, gap, -1).Select(i => new PayerPlanPeriod
{
Id = KeyMasterOffsetManager.GetKeyOffset(i.PersonId).PayerPlanPeriodId,
PersonId = i.PersonId,
StartDate = i.StartDate,
EndDate = i.EndDate,
PayerSourceValue =
payerPlanPeriod.PayerSourceValue,
FamilySourceValue =
payerPlanPeriod.FamilySourceValue,
PlanSourceValue =
payerPlanPeriod.PlanSourceValue
}));
list.Clear();
payerPlanPeriod = entity;
list.Add(entity);
}
result.AddRange(GetEras(list, gap, -1).Select(i => new PayerPlanPeriod
{
Id = KeyMasterOffsetManager.GetKeyOffset(i.PersonId).PayerPlanPeriodId,
PersonId = i.PersonId,
StartDate = i.StartDate,
EndDate = i.EndDate,
PayerSourceValue =
payerPlanPeriod.PayerSourceValue,
FamilySourceValue =
payerPlanPeriod.FamilySourceValue,
PlanSourceValue =
payerPlanPeriod.PlanSourceValue
}));
return(result);
}
/// <summary>
/// A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular drug.
/// Successive periods of Drug Exposures are combined under certain rules to produce continuous Drug Eras.
/// The Drug Era is populated by pulling from the set of drug exposure. A drug era is therefore understood as exposure to a certain compound over a certain period of time.
/// There will only be one type of persistence window (duration that is allowed to elapse between drug exposures) applied to this CDM, which is 30 days.
/// </summary>
/// <param name="drugExposures">set of drug exposure entities</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of drug era</returns>
public virtual IEnumerable <EraEntity> BuildDrugEra(DrugExposure[] drugExposures, ObservationPeriod[] observationPeriods)
{
foreach (var eraEntity in EraHelper.GetEras(
Clean(drugExposures, observationPeriods, true).Where(d => string.IsNullOrEmpty(d.Domain) || d.Domain == "Drug"), 30, 38000182))
{
eraEntity.Id = KeyMasterOffsetManager.GetKeyOffset(eraEntity.PersonId).DrugEraId;
yield return(eraEntity);
}
}
/// <summary>
/// CONDITION_ERAs are chronological periods of condition occurrence.
/// There will only be one type of persistence window (duration that is allowed to elapse between condition occurrences) applied to this CDM, which is 30 days.
/// CONDITION_END_DATE will be the CONDITION_START_DATE.
/// </summary>
/// <param name="conditionOccurrences">Set of condition occurrence entities</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of condition era</returns>
public virtual IEnumerable <EraEntity> BuildConditionEra(ConditionOccurrence[] conditionOccurrences, ObservationPeriod[] observationPeriods)
{
foreach (var eraEntity in EraHelper.GetEras(
Clean(conditionOccurrences, observationPeriods, true).Where(c => string.IsNullOrEmpty(c.Domain) || c.Domain == "Condition"), 30,
38000247))
{
eraEntity.Id = KeyMasterOffsetManager.GetKeyOffset(eraEntity.PersonId).ConditionEraId;
yield return(eraEntity);
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
foreach (var entity in base.GetConcepts(concept, reader, offset))
{
yield return(new DeviceExposure(entity)
{
Id = offset.GetKeyOffset(entity.PersonId).DeviceExposureId,
UniqueDeviceId = reader.GetString(UniqueDeviceId),
Quantity = reader.GetInt(Quantity) ?? 0
});
}
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
{
return(KeyMasterOffsetManager.GetKeyOffset(_visitEnumerator.Current.PersonId)
.VisitOccurrenceIdChanged
? KeyMasterOffsetManager.GetId(_visitEnumerator.Current.PersonId, _visitEnumerator.Current.Id)
: _visitEnumerator.Current.Id);
}
case 1:
return(_visitEnumerator.Current.PersonId);
case 2:
return(_visitEnumerator.Current.ConceptId);
case 3:
return(_visitEnumerator.Current.StartDate);
case 4:
return(_visitEnumerator.Current.StartTime);
case 5:
return(_visitEnumerator.Current.EndDate);
case 6:
return(_visitEnumerator.Current.EndTime);
case 7:
return(_visitEnumerator.Current.TypeConceptId);
case 8:
return(_visitEnumerator.Current.ProviderId == 0 ? null : _visitEnumerator.Current.ProviderId);
case 9:
return(_visitEnumerator.Current.CareSiteId == 0 ? null : _visitEnumerator.Current.CareSiteId);
case 10:
return(_visitEnumerator.Current.SourceValue);
case 11:
return(_visitEnumerator.Current.SourceConceptId);
default:
throw new NotImplementedException();
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
var de = base.GetConcepts(concept, reader, offset).ToList();
if (de.Count > 0)
{
yield return(new DeviceExposure(de[0])
{
Id = KeyMasterOffsetManager.GetKeyOffset(de[0].PersonId).DeviceExposureId,
UniqueDeviceId = reader.GetString(UniqueDeviceId),
StartTime = de[0].StartTime ?? de[0].StartDate.ToString("HH:mm:ss", CultureInfo.InvariantCulture),
Quantity = reader.GetInt(Quantity) ?? 0
});
}
}
public static List <ObservationPeriod> GetObservationPeriods(int gap, EraEntity[] entities, KeyMasterOffsetManager offset)
{
return
(GetEras(entities, gap, entities[0].TypeConceptId ?? -1).Select(
period =>
new ObservationPeriod
{
Id = offset.GetKeyOffset(period.PersonId).ObservationPeriodId,
PersonId = period.PersonId,
StartDate = period.StartDate,
EndDate = period.EndDate.Value,
TypeConceptId = period.TypeConceptId
}).
ToList());
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
return
(base.GetConcepts(concept, reader, offset)
.Select(
e =>
new Note(e)
{
Id = KeyMasterOffsetManager.GetKeyOffset(e.PersonId).NoteId,
EncodingConceptId = reader.GetInt(EncodingConceptId) ?? 0,
LanguageConceptId = reader.GetInt(LanguageConceptId) ?? 0,
Title = reader.GetString(Title),
Text = reader.GetString(Text),
StartTime = e.StartTime ?? e.StartDate.ToString("HH:mm:ss", CultureInfo.InvariantCulture),
}));
}
public override IEnumerable <VisitCost> BuildVisitCosts(VisitOccurrence[] visitOccurrences)
{
foreach (var c in base.BuildVisitCosts(visitOccurrences).Where(vc => vc.TotalPaid.HasValue))
{
ChunkData.AddCostData(new Cost(c.PersonId)
{
CostId = KeyMasterOffsetManager.GetKeyOffset(c.PersonId).VisitCostId,
CurrencyConceptId = c.CurrencyConceptId,
TypeId = 5031,
Domain = "Visit",
EventId = c.Id,
TotalPaid = c.TotalPaid
});
yield return(c);
}
}
public override IEnumerable <ProcedureCost> BuildProcedureCosts(ProcedureOccurrence[] procedureOccurrences)
{
foreach (var c in base.BuildProcedureCosts(procedureOccurrences))
{
ChunkData.AddCostData(new Cost(c.PersonId)
{
CostId = KeyMasterOffsetManager.GetKeyOffset(c.PersonId).VisitCostId,
CurrencyConceptId = c.CurrencyConceptId,
TypeId = 5032,
Domain = "Procedure",
EventId = c.Id,
TotalPaid = c.TotalPaid,
TotalCharge = c.PaidByCoordinationBenefits
});
yield return(c);
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
int? statusConceptId = 0;
string statusSource = null;
if (Concepts != null)
{
var conditionStatusConcept = Concepts.FirstOrDefault(c => c.Name == "ConditionStatusConceptId");
if (conditionStatusConcept != null)
{
var statusConcepts = conditionStatusConcept.GetConceptIdValues(Vocabulary, conditionStatusConcept.Fields[0], reader);
statusSource = reader.GetString(conditionStatusConcept.Fields[0].Key);
if (statusConcepts.Count > 0)
{
statusConceptId = statusConcepts.Min(c => c.ConceptId);
statusSource = statusConcepts.Min(c => c.SourceCode);
if (string.IsNullOrEmpty(statusSource))
{
statusSource = reader.GetString(conditionStatusConcept.Fields[0].Key);
}
if (string.IsNullOrEmpty(statusSource))
{
statusSource = reader.GetString(conditionStatusConcept.Fields[0].SourceKey);
}
}
}
}
return
(base.GetConcepts(concept, reader, offset)
.Select(
e =>
new ConditionOccurrence(e)
{
Id = offset.GetKeyOffset(e.PersonId).ConditionOccurrenceId,
StatusConceptId = statusConceptId.HasValue ? statusConceptId.Value : 0,
StatusSourceValue = statusSource
}));
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
//var obsConcepts = base.GetConcepts(concept, reader, offset).ToList();
var unitConcept = GetUnitConcept(reader);
int?valueAsConceptId = null;
if (Concepts.Length > 2)
{
var valueConcepts = base.GetConcepts(Concepts[2], reader, null).ToList();
if (valueConcepts.Count > 0)
{
valueAsConceptId = valueConcepts[0].ConceptId;
}
}
else
{
valueAsConceptId = reader.GetInt(ValueAsConceptId);
}
foreach (var entity in base.GetConcepts(concept, reader, offset))
{
yield return(new Measurement(entity)
{
Id = offset.GetKeyOffset(entity.PersonId).MeasurementId,
SourceValue = string.IsNullOrWhiteSpace(entity.SourceValue)
? null
: entity.SourceValue,
RangeLow = reader.GetDecimal(RangeLow),
RangeHigh = reader.GetDecimal(RangeHigh),
ValueAsNumber = reader.GetDecimal(ValueAsNumber),
OperatorConceptId = reader.GetInt(OperatorConceptId) ?? 0,
UnitConceptId = unitConcept.Key ?? 0,
UnitSourceValue = string.IsNullOrWhiteSpace(unitConcept.Value) ? null : unitConcept.Value,
ValueSourceValue = reader.GetString(ValueSourceValue),
ValueAsConceptId = valueAsConceptId ?? 0,
Time = reader.GetString(Time)
});
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
int? statusConceptId = 0;
string statusSource = null;
if (Concepts.Length == 2)
{
var statusConcepts = Concepts[1].GetConceptIdValues(Vocabulary, Concepts[1].Fields[0], reader);
statusSource = reader.GetString(Concepts[1].Fields[0].Key);
if (statusConcepts.Count > 0)
{
statusConceptId = statusConcepts.Min(c => c.ConceptId);
statusSource = statusConcepts.Min(c => c.SourceCode);
if (string.IsNullOrEmpty(statusSource))
{
statusSource = reader.GetString(Concepts[1].Fields[0].Key);
}
if (string.IsNullOrEmpty(statusSource))
{
statusSource = reader.GetString(Concepts[1].Fields[0].SourceKey);
}
}
}
return
(base.GetConcepts(concept, reader, offset)
.Select(
e =>
new ConditionOccurrence(e)
{
Id = KeyMasterOffsetManager.GetKeyOffset(e.PersonId).ConditionOccurrenceId,
StatusConceptId = statusConceptId.HasValue ? statusConceptId.Value : 0,
StartTime = e.StartTime ??
e.StartDate.ToString("HH:mm:ss", CultureInfo.InvariantCulture),
StatusSourceValue = statusSource
}));
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
int?relevantConditionConceptId = null;
int?modifierConceptId = reader.GetInt(ModifierConceptId) ?? 0;
if (Concepts != null)
{
var secondConcept = Concepts.FirstOrDefault(c => c.Name != "ProcedureConceptId");
if (secondConcept != null)
{
var relevantConcepts = secondConcept.GetConceptIdValues(Vocabulary, secondConcept.Fields[0], reader);
if (relevantConcepts.Count > 0)
{
relevantConditionConceptId = relevantConcepts.Min(c => c.ConceptId); //CDM v4
modifierConceptId = relevantConditionConceptId; //CDM v5
}
}
}
var quantity = reader.GetDecimal(Quantity);
int?q = null;
if (quantity.HasValue)
{
q = System.Decimal.ToInt32(quantity.Value);
}
foreach (var e in base.GetConcepts(concept, reader, offset))
{
yield return
(new ProcedureOccurrence(e)
{
Id = offset.GetKeyOffset(e.PersonId).ProcedureOccurrenceId,
ReleventConditionConceptId = relevantConditionConceptId,
ModifierConceptId = modifierConceptId ?? 0,
Quantity = q,
QualifierSourceValue = reader.GetString(QualifierSourceValue)
});
}
}
public ProcedureCost CreateEnity(ProcedureOccurrence procedure, IDataRecord reader,
KeyMasterOffsetManager offset)
{
var paidCopay = reader.GetDecimal(PaidCopay);
var paidCoinsurance = reader.GetDecimal(PaidCoinsurance);
var paidTowardDeductible = reader.GetDecimal(PaidTowardDeductible);
decimal? totalOutOfPocket = null;
if (paidCopay.HasValue && paidCoinsurance.HasValue && paidTowardDeductible.HasValue)
{
totalOutOfPocket = paidCopay + paidCoinsurance + paidTowardDeductible;
}
else if (paidCoinsurance.HasValue && paidTowardDeductible.HasValue)
{
totalOutOfPocket = paidCoinsurance + paidTowardDeductible;
}
PopulateOthersConcepts(reader, out var drgConceptId, out var drgSource, out var revenueCodeConceptId,
out var revenueCodeSource);
return new ProcedureCost(procedure)
{
ProcedureCostId = offset.GetKeyOffset(procedure.PersonId).ProcedureCostId,
PaidCopay = paidCopay,
PaidCoinsurance = paidCoinsurance,
PaidTowardDeductible = paidTowardDeductible,
PaidByPayer = reader.GetDecimal(PaidByPayer),
PaidByCoordinationBenefits = reader.GetDecimal(PaidByCoordinationBenefits),
TotalPaid = reader.GetDecimal(TotalPaid),
TotalOutOfPocket = totalOutOfPocket,
RevenueCodeConceptId = revenueCodeConceptId,
RevenueCodeSourceValue = revenueCodeSource,
DrgConceptId = drgConceptId,
DrgSourceValue = drgSource,
CurrencyConceptId = reader.GetInt(CurrencyConceptId) ?? 0
};
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
foreach (var entity in base.GetConcepts(concept, reader, offset))
{
var unitConcept = GetUnitConcept(reader, "UnitConceptId");
var qualifierConcept = GetUnitConcept(reader, "QualifierConceptId");
var createObservation = new Func <Observation>(() => new Observation(entity)
{
Id = offset.GetKeyOffset(entity.PersonId).ObservationId,
SourceValue = string.IsNullOrWhiteSpace(entity.SourceValue)
? null
: entity.SourceValue,
RangeLow = reader.GetDecimal(RangeLow),
RangeHigh = reader.GetDecimal(RangeHigh),
UnitsConceptId = unitConcept.Key ?? 0,
UnitsSourceValue = string.IsNullOrWhiteSpace(unitConcept.Value) ? null : unitConcept.Value,
ValueAsConceptId = reader.GetInt(ValueAsConceptId) ?? 0,
QualifierConceptId = qualifierConcept.Key ?? 0,
QualifierSourceValue = string.IsNullOrWhiteSpace(qualifierConcept.Value) ? null : qualifierConcept.Value,
//RelevantConditionConceptId = relevantConditionConceptId ?? 0
});
var observation = createObservation();
observation.ValueAsNumber = reader.GetDecimal(ValueAsNumber);
if (observation.ValueAsNumber.HasValue)
{
observation.ValueAsNumber = Math.Round(observation.ValueAsNumber.Value, 3);
}
observation.ValueAsString = reader.GetString(ValueAsString);
yield return(observation);
}
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
{
return(_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged
? _offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id)
: _enumerator.Current.Id);
}
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.StartDate);
case 5:
return(_enumerator.Current.EndDate);
case 6:
return(_enumerator.Current.EndDate);
case 7:
return(_enumerator.Current.TypeConceptId);
case 8:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 9:
return(_enumerator.Current.CareSiteId == 0 ? null : _enumerator.Current.CareSiteId);
case 10:
return(_enumerator.Current.SourceValue);
case 11:
return(_enumerator.Current.SourceConceptId);
case 12:
return(_enumerator.Current.AdmittingSourceConceptId);
case 13:
return(_enumerator.Current.AdmittingSourceValue);
case 14:
return(_enumerator.Current.DischargeToConceptId);
case 15:
return(_enumerator.Current.DischargeToSourceValue);
case 16:
if (_enumerator.Current.PrecedingVisitOccurrenceId.HasValue)
{
if (_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.PrecedingVisitOccurrenceId.Value));
}
return(_enumerator.Current.PrecedingVisitOccurrenceId);
}
return(_enumerator.Current.PrecedingVisitOccurrenceId);
default:
throw new NotImplementedException();
}
}
public object GetValue(int i)
{
if (_enumerator.Current == null)
{
return(null);
}
switch (i)
{
case 0:
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.CostId)); //TODO VisitCostOffset -> CostOffset
case 1:
return(_enumerator.Current.PersonId);
case 2:
if (_enumerator.Current.Domain == "Visit" && !_offset
.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(_enumerator.Current.EventId);
}
return(_offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.EventId));
case 3:
return(_enumerator.Current.EventFieldConceptId);
case 4:
return(_enumerator.Current.CostConceptId);
case 5:
return(_enumerator.Current.TypeId);
case 6:
return(_enumerator.Current.CurrencyConceptId);
case 7:
return(_enumerator.Current.CostValue.Round());
case 8:
return(_enumerator.Current.IncurredDate);
case 9:
return(_enumerator.Current.BilledDate);
case 10:
return(_enumerator.Current.PaidDate);
case 11:
return(_enumerator.Current.RevenueCodeConceptId);
case 12:
return(_enumerator.Current.DrgConceptId);
case 13:
return(_enumerator.Current.SourceValue);
case 14:
return(_enumerator.Current.SourceConceptId);
case 15:
return(_enumerator.Current.RevenueCodeSourceValue);
case 16:
return(_enumerator.Current.DrgSourceValue);
case 17:
return(_enumerator.Current.PayerPlanPeriodId.HasValue
? _offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.PayerPlanPeriodId.Value)
: _enumerator.Current.PayerPlanPeriodId);
default:
throw new NotImplementedException();
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager offset)
{
foreach (var entity in base.GetConcepts(concept, reader, offset))
{
var unitConcept = GetUnitConcept(reader);
int?relevantConditionConceptId = null;
if (Concepts.Length == 3)
{
var relevantConditionConcepts =
Concepts[2].GetConceptIdValues(Vocabulary, Concepts[2].Fields[0], reader);
if (relevantConditionConcepts.Count > 0)
{
relevantConditionConceptId = relevantConditionConcepts.Min(c => c.ConceptId);
}
}
var createObservation = new Func <Observation>(() => new Observation(entity)
{
Id = offset.GetKeyOffset(entity.PersonId).ObservationId,
SourceValue = string.IsNullOrWhiteSpace(entity.SourceValue)
? null
: entity.SourceValue,
RangeLow = reader.GetDecimal(RangeLow),
RangeHigh = reader.GetDecimal(RangeHigh),
UnitsConceptId = unitConcept.Key ?? 0,
UnitsSourceValue = string.IsNullOrWhiteSpace(unitConcept.Value) ? null : unitConcept.Value,
ValueAsConceptId = reader.GetInt(ValueAsConceptId) ?? 0,
QualifierConceptId = reader.GetInt(QualifierConceptId) ?? 0,
QualifierSourceValue = reader.GetString(QualifierSourceValue),
RelevantConditionConceptId = relevantConditionConceptId ?? 0
});
if (ValuesAsNumber != null && ValuesAsNumber.Length > 1)
{
foreach (var valueAsNumber in ValuesAsNumber)
{
var value = reader.GetDecimal(valueAsNumber);
if (value != null)
{
var observation = createObservation();
observation.ValueAsNumber = Math.Round(value.Value, 3);
observation.SourceValue = observation.ValueAsNumber.ToString();
observation.TypeConceptId = 38000277;
yield return(observation);
}
}
}
else if (ValuesAsString != null && ValuesAsString.Length > 1)
{
foreach (var valueAsString in ValuesAsString)
{
var value = reader.GetString(valueAsString);
if (!string.IsNullOrEmpty(value) && value != "-" && value != "9") //TMP
{
var observation = createObservation();
observation.ValueAsString = reader.GetString(valueAsString);
observation.SourceValue = valueAsString;
observation.TypeConceptId = 38000278;
yield return(observation);
}
}
}
//else if (obsConcepts[0].ConceptId > 0 || !string.IsNullOrEmpty(obsConcepts[0].SourceValue))
else if (entity.ConceptId > 0 || concept.Fields[0].IsNullable || !string.IsNullOrEmpty(entity.SourceValue))
{
var observation = createObservation();
if (ValuesAsNumber != null && ValuesAsNumber.Length > 0)
{
observation.ValueAsNumber = reader.GetDecimal(ValuesAsNumber[0]);
if (observation.ValueAsNumber.HasValue)
{
observation.ValueAsNumber = Math.Round(observation.ValueAsNumber.Value, 3);
}
}
if (ValuesAsString != null && ValuesAsString.Length > 0)
{
observation.ValueAsString = reader.GetString(ValuesAsString[0]);
// Workaround, map ValueAsString (usind SourceLookup) and reset SourceValue to original value
if (observation.AdditionalFields != null &&
observation.AdditionalFields.ContainsKey("original_source"))
{
observation.ValueAsString = observation.SourceValue;
observation.SourceValue = observation.AdditionalFields["original_source"];
}
}
yield return(observation);
}
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
DateTime?endDate = null;
int routeConceptId = 0;
string routeSourceValue = null;
if (Concepts != null)
{
var routeConcept = Concepts.FirstOrDefault(c => c.Name == "RouteConceptId");
if (routeConcept != null)
{
var routeConcepts = base.GetConcepts(routeConcept, reader, null).ToList();
routeSourceValue = reader.GetString(routeConcept.Fields[0].Key);
if (routeConcepts.Count > 0)
{
routeConceptId = routeConcepts[0].ConceptId;
routeSourceValue = routeConcepts[0].SourceValue;
}
}
}
else
{
routeConceptId = reader.GetInt(RouteConceptId) ?? 0;
routeSourceValue = reader.GetString(RouteSourceValue);
}
foreach (var c in base.GetConcepts(concept, reader, offset))
{
var e = (Entity)c;
var calculatedDaysSupply = reader.GetInt(DaysSupply) ?? 0;
if (!string.IsNullOrEmpty(EndDate))
{
if (calculatedDaysSupply > 0 && calculatedDaysSupply <= 365)
{
endDate = e.StartDate.AddDays(calculatedDaysSupply - 1);
}
else
{
endDate = reader.GetDateTime(EndDate);
}
}
var verbatimEndDate = reader.GetDateTime(VerbatimEndDate);
yield return(new DrugExposure(e)
{
Id = offset.GetKeyOffset(e.PersonId).DrugExposureId,
Refills = reader.GetIntSafe(Refill),
DaysSupply = reader.GetInt(DaysSupply),
CalculatedDaysSupply = calculatedDaysSupply,
Quantity = reader.GetDecimal(Quantity),
Sig = reader.GetString(Sig),
EndDate = endDate == DateTime.MinValue ? null : endDate,
VerbatimEndDate = verbatimEndDate == DateTime.MinValue ? (DateTime?)null : verbatimEndDate,
RouteConceptId = routeConceptId,
RouteSourceValue = routeSourceValue,
DoseUnitConceptId = reader.GetInt(DoseUnitConceptId) ?? 0,
DoseUnitSourceValue = reader.GetString(DoseUnitSourceValue),
StopReason = reader.GetString(StopReason)
});
}
}
public object GetValue(int i)
{
if (_enumerator.Current == null)
{
return(null);
}
switch (i)
{
case 0:
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.EndDate);
case 5:
return(_enumerator.Current.TypeConceptId);
case 6:
return(_enumerator.Current.StopReason);
case 7:
return(_enumerator.Current.Refills);
case 8:
return(_enumerator.Current.Quantity);
case 9:
return(_enumerator.Current.DaysSupply);
case 10:
return(_enumerator.Current.Sig);
case 11:
return(_enumerator.Current.RouteConceptId);
case 12:
return(_enumerator.Current.EffectiveDrugDose);
case 13:
return(_enumerator.Current.DoseUnitConceptId);
case 14:
return(_enumerator.Current.LotNumber);
case 15:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 16:
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (KeyMasterOffsetManager.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(KeyMasterOffsetManager.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
case 17:
return(_enumerator.Current.SourceValue);
case 18:
return(_enumerator.Current.SourceConceptId);
case 19:
return(_enumerator.Current.RouteSourceValue);
case 20:
return(_enumerator.Current.DoseUnitSourceValue);
default:
throw new NotImplementedException();
}
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
return(_offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.Time);
case 5:
return(_enumerator.Current.TypeConceptId);
case 6:
return(_enumerator.Current.OperatorConceptId);
case 7:
return(_enumerator.Current.ValueAsNumber);
case 8:
return(_enumerator.Current.ValueAsConceptId);
case 9:
return(_enumerator.Current.UnitConceptId);
case 10:
return(_enumerator.Current.RangeLow);
case 11:
return(_enumerator.Current.RangeHigh);
case 12:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 13:
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
case 14:
return(_enumerator.Current.SourceValue);
case 15:
return(_enumerator.Current.SourceConceptId);
case 16:
return(_enumerator.Current.UnitSourceValue);
case 17:
return(_enumerator.Current.ValueSourceValue);
default:
throw new NotImplementedException();
}
}
public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
{
Offset = o;
ChunkData = data;
var result = BuildPerson(PersonRecords.ToList());
var person = result.Key;
if (person == null)
{
Complete = true;
return(result.Value);
}
var observationPeriods =
BuildObservationPeriods(9999, ObservationPeriodsRaw.ToArray())
.ToArray();
if (Excluded(person, observationPeriods))
{
Complete = true;
return(Attrition.ImplausibleYOBPostEarliestOP);
}
var visitDetails = BuildVisitDetails(null, VisitOccurrencesRaw.ToArray(), observationPeriods).ToArray();
var visitOccurrences = new Dictionary <long, VisitOccurrence>();
var visitIds = new List <long>();
foreach (var visitOccurrence in BuildVisitOccurrences(VisitOccurrencesRaw.ToArray(), observationPeriods))
{
if (visitOccurrence.IdUndefined)
{
visitOccurrence.Id = Offset.GetKeyOffset(visitOccurrence.PersonId).VisitOccurrenceId;
visitOccurrence.IdUndefined = false;
}
if (!visitOccurrences.ContainsKey(visitOccurrence.Id))
{
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
visitIds.Add(visitOccurrence.Id);
}
var ecntrId = visitOccurrence.AdditionalFields["ecntr_id"];
if (long.TryParse(ecntrId, out var visitId))
{
if (!_visitIdMap.ContainsKey(visitId))
{
_visitIdMap.Add(visitId, new List <VisitOccurrence>());
}
_visitIdMap[visitId].Add(visitOccurrence);
}
}
foreach (var visitDetail in visitDetails)
{
var vo = GetVisitOccurrence(visitDetail);
visitDetail.VisitOccurrenceId = vo?.Id ?? 0;
}
long?prevVisitId = null;
foreach (var visitId in visitIds.OrderBy(v => v))
{
if (prevVisitId.HasValue)
{
visitOccurrences[visitId].PrecedingVisitOccurrenceId = prevVisitId;
}
prevVisitId = visitId;
}
foreach (var e in ConditionOccurrencesRaw)
{
SetVisitId(e);
}
foreach (var e in ProcedureOccurrencesRaw)
{
SetVisitId(e);
}
foreach (var e in ObservationsRaw)
{
SetVisitId(e);
}
foreach (var e in DrugExposuresRaw)
{
SetVisitId(e);
}
foreach (var e in MeasurementsRaw)
{
SetVisitId(e);
}
foreach (var e in DeviceExposureRaw)
{
SetVisitId(e);
}
var conditionOccurrences =
BuildConditionOccurrences(ConditionOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
foreach (var co in conditionOccurrences)
{
co.Id = Offset.GetKeyOffset(co.PersonId).ConditionOccurrenceId;
}
var procedureOccurrences =
BuildProcedureOccurrences(ProcedureOccurrencesRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
foreach (var procedureOccurrence in procedureOccurrences)
{
procedureOccurrence.Id =
Offset.GetKeyOffset(procedureOccurrence.PersonId).ProcedureOccurrenceId;
}
var observations = BuildObservations(ObservationsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
foreach (var ob in observations)
{
ob.Id = Offset.GetKeyOffset(ob.PersonId).ObservationId;
}
var drugExposures =
BuildDrugExposures(DrugExposuresRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var measurements = BuildMeasurement(MeasurementsRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
var deviceExposure = BuildDeviceExposure(DeviceExposureRaw.ToArray(), visitOccurrences, observationPeriods)
.ToArray();
// set corresponding ProviderIds
SetProviderIds(drugExposures);
SetProviderIds(conditionOccurrences);
SetProviderIds(visitOccurrences.Values.ToArray());
SetProviderIds(procedureOccurrences);
SetProviderIds(observations);
SetProviderIds(visitDetails);
// push built entities to ChunkBuilder for further save to CDM database
AddToChunk(person, null,
observationPeriods,
new PayerPlanPeriod[0],
drugExposures,
conditionOccurrences,
procedureOccurrences,
observations,
measurements,
visitOccurrences.Values.ToArray(), visitDetails, new Cohort[0], deviceExposure, new Note[0]);
Complete = true;
return(Attrition.None);
}
// is this called only because the datatype specific methods are not implemented?
// probably performance to be gained by not passing object back?
public object GetValue(int i)
{
switch (i)
{
case 0:
return(_offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.Id));
case 1:
return(_enumerator.Current.PersonId);
case 2:
return(_enumerator.Current.ConceptId);
case 3:
return(_enumerator.Current.StartDate);
case 4:
return(_enumerator.Current.StartDate.TimeOfDay);
case 5:
return(_enumerator.Current.TypeConceptId);
case 6:
return(_enumerator.Current.ValueAsNumber);
case 7:
return(_enumerator.Current.ValueAsString);
case 8:
return(_enumerator.Current.ValueAsConceptId);
case 9:
return(_enumerator.Current.QualifierConceptId);
case 10:
return(_enumerator.Current.UnitsConceptId);
case 11:
return(_enumerator.Current.ProviderId == 0 ? null : _enumerator.Current.ProviderId);
case 12:
if (_enumerator.Current.VisitOccurrenceId.HasValue)
{
if (_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
{
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitOccurrenceId.Value));
}
return(_enumerator.Current.VisitOccurrenceId.Value);
}
return(null);
case 13:
if (_enumerator.Current.VisitDetailId.HasValue)
{
if (_offset.GetKeyOffset(_enumerator.Current.PersonId).VisitDetailIdChanged)
{
return(_offset.GetId(_enumerator.Current.PersonId,
_enumerator.Current.VisitDetailId.Value));
}
return(_enumerator.Current.VisitDetailId);
}
return(null);
case 14:
return(_enumerator.Current.SourceValue);
case 15:
return(_enumerator.Current.SourceConceptId);
case 16:
return(_enumerator.Current.UnitsSourceValue);
case 17:
return(_enumerator.Current.QualifierSourceValue);
case 18:
return(_enumerator.Current.EventId);
case 19:
return(_enumerator.Current.EventFieldConceptId);
case 20:
return(_enumerator.Current.ValueAsDatetime);
default:
throw new NotImplementedException();
}
}
