/// <summary>
/// Projects Enumeration of drug exposure from the raw set of drug exposure entities.
/// During build:
/// override the drug's start/end date using the end date of the corresponding observation period.
/// </summary>
/// <param name="drugExposures">raw set of drug exposures entities</param>
/// <param name="visitOccurrences">the visit occurrences entities for current person</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of drug exposure entities</returns>
public override IEnumerable<DrugExposure> BuildDrugExposures(DrugExposure[] drugExposures,
Dictionary<long, VisitOccurrence> visitOccurrences,
ObservationPeriod[] observationPeriods)
{
if (observationPeriods.Length != 0)
{
foreach (var drugExposure in drugExposures)
{
drugExposure.StartDate = drugExposure.DaysSupply.HasValue
? observationPeriods[0].EndDate.AddDays(drugExposure.DaysSupply.Value*-1)
: observationPeriods[0].EndDate;
drugExposure.EndDate = observationPeriods[0].EndDate;
yield return drugExposure;
}
}
}
/// <summary>
/// Projects Enumeration of ConditionOccurrence from the raw set of ConditionOccurrence entities.
/// During build:
/// override the condition's start date using the end date of the corresponding observation period.
/// </summary>
/// <param name="conditionOccurrences">raw set of condition occurrence entities</param>
/// <param name="visitOccurrences">the visit occurrence entities for current person</param>
/// <param name="observationPeriods">the observation period entities for current person</param>
/// <returns>Enumeration of condition occurrence entities</returns>
public override IEnumerable<ConditionOccurrence> BuildConditionOccurrences(
ConditionOccurrence[] conditionOccurrences, Dictionary<long, VisitOccurrence> visitOccurrences,
ObservationPeriod[] observationPeriods)
{
if (observationPeriods.Length != 0)
{
foreach (var conditionOccurrence in conditionOccurrences)
{
var sourceValue = conditionOccurrence.SourceValue;
if (sourceValue.Length < 2) continue;
if (sourceValue.Substring(sourceValue.Length - 2) != "_1") continue;
if (conditionOccurrence.ConceptId > 0)
{
conditionOccurrence.StartDate = observationPeriods[0].StartDate;
conditionOccurrence.EndDate = null;
yield return conditionOccurrence;
}
}
}
}
/// <summary>
/// Projects Enumeration of ConditionOccurrence from the raw set of ConditionOccurrence entities.
/// During build:
/// override the condition's start date using the start date of the corresponding visit.
/// overide TypeConceptId per CDM Mapping spec.
/// </summary>
/// <param name="conditionOccurrences">raw set of condition occurrence entities</param>
/// <param name="vo">the visit occurrence entities for current person</param>
/// <param name="op">the observation period entities for current person</param>
/// <returns>Enumeration of condition occurrence entities</returns>
public override IEnumerable<ConditionOccurrence> BuildConditionOccurrences(ConditionOccurrence[] conditionOccurrences, Dictionary<long, VisitOccurrence> vo, ObservationPeriod[] op)
{
var result = new HashSet<ConditionOccurrence>();
var dateClaimTypeDictionary = new Dictionary<DateTime, Dictionary<string, List<IEntity>>>();
foreach (var conditionOccurrence in conditionOccurrences)
{
var visitOccurrence = GetVisitOccurrence(conditionOccurrence);
if (visitOccurrence == null)
continue;
conditionOccurrence.VisitOccurrenceId = visitOccurrence.Id;
conditionOccurrence.StartDate = visitOccurrence.StartDate;
conditionOccurrence.EndDate = null;
conditionOccurrence.TypeConceptId = GetConditionTypeConceptId(conditionOccurrence.TypeConceptId.Value, visitOccurrence.ConceptId);
AddToDateClaimTypeDictionary(dateClaimTypeDictionary, conditionOccurrence, visitOccurrence);
}
foreach (var sameStartDate in conditionOccurrences.Where(c => c.VisitOccurrenceId.HasValue && !string.IsNullOrEmpty(c.SourceValue)).GroupBy(c => c.StartDate))
{
foreach (var sameVisit in sameStartDate.GroupBy(c => c.VisitOccurrenceId))
{
foreach (var sameSource in sameVisit.GroupBy(c => c.SourceValue))
{
foreach (var sameConcept in sameSource.GroupBy(c => c.ConceptId))
{
var conditionOccurrence = sameConcept.OrderBy(c => c.TypeConceptId).ToList()[0];
if (!CodeValidator.IsValidIcd9(conditionOccurrence.SourceValue)) continue;
conditionOccurrence.ProviderKey = GetProviderKey(vo[conditionOccurrence.VisitOccurrenceId.Value],
conditionOccurrence, dateClaimTypeDictionary);
result.Add(conditionOccurrence);
}
}
}
}
return base.BuildConditionOccurrences(result.ToArray(), vo, op);
}
private static IEnumerable<VisitOccurrence> CleanVisitOccurrences(IEnumerable<VisitOccurrence> visitOccurrences, ObservationPeriod[] observationPeriods)
{
foreach (var visitOccurrence in visitOccurrences)
{
if (!visitOccurrence.EndDate.HasValue || visitOccurrence.EndDate < visitOccurrence.StartDate)
visitOccurrence.EndDate = visitOccurrence.StartDate;
var observationPeriod = observationPeriods.FirstOrDefault(op => visitOccurrence.StartDate.Between(op.StartDate, op.EndDate) || visitOccurrence.EndDate.Value.Between(op.StartDate, op.EndDate));
if (observationPeriod == null) continue;
if (visitOccurrence.StartDate < observationPeriod.StartDate)
visitOccurrence.StartDate = observationPeriod.StartDate;
if (visitOccurrence.EndDate > observationPeriod.EndDate)
visitOccurrence.EndDate = observationPeriod.EndDate;
yield return visitOccurrence;
}
}
/// <summary>
/// Projects Enumeration of Visit Occurrence from the raw set of Visit Occurrence entities.
/// </summary>
/// <param name="rawVisitOccurrences">raw set of Visit Occurrence entities</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of Visit Occurrence</returns>
public override IEnumerable<VisitOccurrence> BuildVisitOccurrences(VisitOccurrence[] rawVisitOccurrences, ObservationPeriod[] observationPeriods)
{
var visitOccurrences = CleanVisitOccurrences(rawVisitOccurrences, observationPeriods).ToList();
var ipVisits = GetIPClaims(visitOccurrences).ToList();
var erVisits = new List<VisitOccurrence>();
var opVisits = new List<VisitOccurrence>();
foreach (var visitOccurrence in visitOccurrences.Where(visitOccurrence => visitOccurrence.ConceptId != 9201))
{
var ip = ipVisits.FirstOrDefault(v => visitOccurrence.StartDate.Between(v.StartDate, v.EndDate.Value));
if (visitOccurrence.ConceptId == 9203)
{
if (ip == null || (visitOccurrence.StartDate == ip.StartDate && visitOccurrence.EndDate == ip.StartDate))
//ER - 9203
{
erVisits.Add(visitOccurrence);
}
else
{
if (!rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid))
rawVisits.Add(visitOccurrence.SourceRecordGuid, ip);
}
}
else if (ip == null)
{
opVisits.Add(visitOccurrence);
}
else
{
if (!rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid))
rawVisits.Add(visitOccurrence.SourceRecordGuid, ip);
}
}
foreach (var ipVisit in ipVisits)
{
yield return ipVisit;
}
// collapse claims with the same FST_DT in ER table as one unique ER visit
foreach (var patplanidGroup in erVisits.GroupBy(vo => vo.AdditionalFields["pat_planid"]))
{
foreach (var erGroup in patplanidGroup.GroupBy(v => v.StartDate))
{
var visit = erGroup.First();
visit.EndDate = erGroup.Max(v => v.EndDate);
foreach (
var visitOccurrence in
erGroup.Where(visitOccurrence => !rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid)))
{
rawVisits.Add(visitOccurrence.SourceRecordGuid, visit);
}
yield return visit;
}
}
foreach (var patplanidGroup in opVisits.GroupBy(vo => vo.AdditionalFields["pat_planid"]))
{
foreach (var opGroup in patplanidGroup.GroupBy(v => v.StartDate))
{
foreach (var opGroup1 in opGroup.GroupBy(v => v.AdditionalFields["prov"]))
{
var visit = opGroup1.First();
visit.EndDate = opGroup1.Max(v => v.EndDate);
foreach (
var visitOccurrence in
opGroup1.Where(visitOccurrence => !rawVisits.ContainsKey(visitOccurrence.SourceRecordGuid))
)
{
rawVisits.Add(visitOccurrence.SourceRecordGuid, visit);
}
yield return visit;
}
}
}
}
/// <summary>
/// Projects Enumeration of ProcedureOccurrence from the raw set of ProcedureOccurence entities.
/// During build:
/// override the procedure's start date using the end date of the corresponding visit.
/// overide TypeConceptId per CDM Mapping spec.
/// truncate procedure's dates to the corresponding observation period dates
/// </summary>
/// <param name="procedureOccurrences">raw set of procedure occurrence entities</param>
/// <param name="visitOccurrences">the visit occurrence entities for current person</param>
/// <param name="observationPeriods">the observation period entities for current person</param>
/// <returns>Enumeration of procedure occurrence entities</returns>
public override IEnumerable<ProcedureOccurrence> BuildProcedureOccurrences(ProcedureOccurrence[] procedureOccurrences, Dictionary<long, VisitOccurrence> visitOccurrences, ObservationPeriod[] observationPeriods)
{
var result = new HashSet<ProcedureOccurrence>();
var cost = new Dictionary<ProcedureOccurrence, List<ProcedureCost>>();
var dateClaimTypeDictionary = new Dictionary<DateTime, Dictionary<string, List<IEntity>>>();
var cdProcedures = new List<ProcedureOccurrence>();
var otherProcedures = new List<ProcedureOccurrence>();
foreach (var procedureOccurrence in procedureOccurrences)
{
var visitOccurrence = GetVisitOccurrence(procedureOccurrence);
if (visitOccurrence == null)
continue;
procedureOccurrence.VisitOccurrenceId = visitOccurrence.Id;
var observationPeriod = observationPeriods.FirstOrDefault(op => op.StartDate.Between(procedureOccurrence.StartDate, procedureOccurrence.EndDate.Value) || op.EndDate.Between(procedureOccurrence.StartDate, procedureOccurrence.EndDate.Value));
if (observationPeriod != null)
{
if (procedureOccurrence.StartDate < observationPeriod.StartDate)
procedureOccurrence.StartDate = observationPeriod.StartDate;
if (procedureOccurrence.StartDate > observationPeriod.EndDate)
procedureOccurrence.StartDate = observationPeriod.EndDate;
}
procedureOccurrence.EndDate = null;
procedureOccurrence.TypeConceptId = GetProcedureTypeConceptId(procedureOccurrence.TypeConceptId.Value, visitOccurrence.ConceptId);
if (procedureOccurrence.TypeConceptId == 38000272 || procedureOccurrence.TypeConceptId == 38000254)
{
if (procedureOccurrence.ProcedureCosts != null)
{
if (!cost.ContainsKey(procedureOccurrence))
cost.Add(procedureOccurrence, new List<ProcedureCost>());
cost[procedureOccurrence].AddRange(procedureOccurrence.ProcedureCosts);
}
cdProcedures.Add(procedureOccurrence);
}
else
{
procedureOccurrence.StartDate = visitOccurrence.EndDate.Value;
if (CodeValidator.IsValidIcd9Procedure(procedureOccurrence.SourceValue))
otherProcedures.Add(procedureOccurrence);
}
AddToDateClaimTypeDictionary(dateClaimTypeDictionary, procedureOccurrence, visitOccurrence);
}
foreach (var procedureOccurrence in BuildProceduresCd(cdProcedures, cost))
{
result.Add(procedureOccurrence);
}
foreach (var procedureOccurrence in BuildProceduresOther(otherProcedures, visitOccurrences, dateClaimTypeDictionary))
{
result.Add(procedureOccurrence);
}
return base.BuildProcedureOccurrences(result.ToArray(), visitOccurrences, observationPeriods);
}
/// <summary>
/// Projects Enumeration of drug exposure from the raw set of drug exposure & procedure occurrence entities.
/// During build:
/// overide TypeConceptId per CDM Mapping spec.
/// </summary>
/// <param name="de">raw set of drug exposures entities</param>
/// <param name="visitOccurrences">the visit occurrences entities for current person</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of drug exposure entities</returns>
public override IEnumerable<DrugExposure> BuildDrugExposures(DrugExposure[] de, Dictionary<long, VisitOccurrence> visitOccurrences, ObservationPeriod[] observationPeriods)
{
var drugExposures = PrepareDrugExposures(de, visitOccurrences).ToArray();
return base.BuildDrugExposures(drugExposures, visitOccurrences, observationPeriods);
}
/// <summary>
/// Projects death entity from the raw set of death entities.
/// </summary>
/// <param name="deathRaw">raw set of death entities</param>
/// <param name="visitOccurrences">the visit occurrence entities for current person</param>
/// <param name="observationPeriods">the observation period entities for current person</param>
/// <returns>death entity</returns>
public override Death BuildDeath(Death[] deathRaw, Dictionary<long, VisitOccurrence> visitOccurrences, ObservationPeriod[] observationPeriods)
{
var death = FilterDeathRecords(deathRaw).ToList();
if (death.Any())
{
var maxStartDate = death.Max(d => d.StartDate);
var result = death.Where(d => d.StartDate == maxStartDate).OrderByDescending(d => d.Primary).First();
result.CauseConceptId = 0;
var maxVisitStartDate = visitOccurrences.Values.Max(vo => vo.StartDate);
if (maxVisitStartDate < result.StartDate.AddDays(32))
{
return result;
}
}
return null;
}
/// <summary>
/// Projects Enumeration of Observations from the raw set of Observation entities.
/// During build:
/// override the observations start date using the start date of the corresponding observation period.
/// </summary>
/// <param name="observations">raw set of observations entities</param>
/// <param name="visitOccurrences">the visit occurrences entities for current person</param>
/// <param name="observationPeriods">the observation periods entities for current person</param>
/// <returns>Enumeration of Observation from the raw set of Observation entities</returns>
public override IEnumerable<Observation> BuildObservations(Observation[] observations,
Dictionary<long, VisitOccurrence> visitOccurrences,
ObservationPeriod[] observationPeriods)
{
if (observationPeriods.Length != 0)
{
var unique = new HashSet<Observation>();
foreach (var observation in observations)
{
if (observation.ConceptId == -999) continue;
observation.StartDate = observationPeriods[0].StartDate;
observation.ValueAsConceptId = Convert.ToInt32(observation.UnitsConceptId);
observation.UnitsConceptId = null;
observation.UnitsSourceValue = null;
unique.Add(observation);
}
foreach (var observation in unique)
{
yield return observation;
}
}
}
