/// <summary>
/// Build person entity and all person related entities like: DrugExposures, ConditionOccurrences, ProcedureOccurrences... from raw data sets
/// </summary>
public virtual Attrition Build(ChunkData data, KeyMasterOffsetManager o)
{
this.Offset = o;
this.ChunkData = data;
var result = BuildPerson(PersonRecords.ToList());
var person = result.Key;
if (person == null)
{
Complete = true;
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))
{
Complete = true;
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 = KeyMasterOffsetManager.GetKeyOffset(visitOccurrence.PersonId).VisitOccurrenceId;
}
visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
}
var visitDetails = BuildVisitDetails(VisitDetailsRaw.ToArray(), VisitOccurrencesRaw.ToArray(),
observationPeriods).ToArray();
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);
// TODO: TMP
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(), visitDetails, cohort, deviceExposure, notes);
Complete = true;
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);
}
/// <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 offset)
{
Offset = offset;
ChunkData = data;
var p = new List <Person>();
var op = new List <ObservationPeriod>();
var vo = new List <VisitOccurrence>();
var co = new List <ConditionOccurrence>();
var de = new List <DrugExposure>();
var o = new List <Observation>();
foreach (var record in PersonRecords)
{
var table = record.AdditionalFields["table_name"]?.ToLower();
var variable = record.AdditionalFields["variable"]?.ToLower();
var value = record.AdditionalFields["value"]?.ToLower();
var description = string.Empty;
if (record.AdditionalFields.ContainsKey("value_description"))
{
description = record.AdditionalFields["value_description"]?.ToLower();
}
if (string.IsNullOrEmpty(table) || string.IsNullOrEmpty(variable))
{
continue;
}
decimal?decimalValue = null;
if (decimal.TryParse(value, out var dValue))
{
decimalValue = dValue;
}
var valueAsString = value;
if (!string.IsNullOrEmpty(description))
{
valueAsString = description;
}
var year = 2000;
if (table.StartsWith("demo"))
{
p.Add(record);
// GetYear => empty -> 2000 'B' -> 2002, 'C' -> 2004, 'D' -> 2006 ....
year = GetYear(table.Replace("demo", "").Replace("_", ""));
if (op.Count == 0)
{
op.Add(new ObservationPeriod
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).ObservationId,
PersonId = record.PersonId,
TypeConceptId = 0,
StartDate = new DateTime(year - 1, 1, 1),
EndDate = new DateTime(year, 12, 31)
});
vo.Add(new VisitOccurrence(record)
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).VisitOccurrenceId,
ConceptId = 0,
StartDate = new DateTime(year - 1, 1, 1),
StartTime = new DateTime(year - 1, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
EndDate = new DateTime(year - 1, 1, 1),
EndTime = new DateTime(year - 1, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
TypeConceptId = 44818519
});
}
}
else if (table.StartsWith("rxq_rx") && (variable.StartsWith("rxddrgid") || variable.StartsWith("rxddrug")))
{
year = GetYear(table.Replace("rxq_rx", "").Replace("_", ""));
string sourceValue = null;
if (!string.IsNullOrEmpty(value) && value.Contains('_'))
{
var values = value.Split('_');
// use the characters after the last underscore(_)
// 60000_1_7__d00910
if (table == "rxq_rx" || table == "rxq_rx_b")
{
sourceValue = values.Last();
}
// use the characters before the first underscore (_)
// d00848_365_1_DICLOFENAC
else
{
sourceValue = values[0];
}
}
var result = Vocabulary.Lookup(sourceValue, "Drug", DateTime.MinValue);
if (result.Any())
{
foreach (var lookupValue in result)
{
var conceptId = lookupValue.ConceptId;
if (conceptId.HasValue)
{
de.Add(new DrugExposure(record)
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).DrugExposureId,
ConceptId = conceptId.Value,
StartDate = new DateTime(year - 1, 1, 1),
StartTime = new DateTime(year - 1, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
EndDate = new DateTime(year - 1, 1, 1),
EndTime = new DateTime(year - 1, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
SourceValue = sourceValue,
TypeConceptId = 44787730
});
}
}
}
}
else if (!string.IsNullOrEmpty(value))
{
var yearField = table.Split('_').Last();
year = GetYear(yearField == table ? null : yearField);
var sourceValue = variable + "_" + value;
if (variable == "bmxbmi")
{
int?conceptId = null;
if (double.TryParse(value, out var bmxbmi))
{
if (bmxbmi < 18.5)
{
conceptId = 435372;
}
else if (bmxbmi > 25.0 && bmxbmi < 29.9)
{
conceptId = 437525;
}
else
{
conceptId = 4215968;
}
}
co.Add(new ConditionOccurrence(record)
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).ConditionOccurrenceId,
ConceptId = conceptId.Value,
StartDate = new DateTime(year, 1, 1),
StartTime = new DateTime(year, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
EndDate = null,
EndTime = null,
TypeConceptId = 45905770,
SourceValue = sourceValue
});
}
else
{
var result = Vocabulary.Lookup(sourceValue, "Condition", DateTime.MinValue);
if (result.Any())
{
foreach (var lookupValue in result)
{
var conceptId = lookupValue.ConceptId;
if (conceptId.HasValue)
{
co.Add(new ConditionOccurrence(record)
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).ConditionOccurrenceId,
ConceptId = conceptId.Value,
StartDate = new DateTime(year, 1, 1),
StartTime = new DateTime(year, 1, 1).ToString("HH:mm:ss",
CultureInfo.InvariantCulture),
EndDate = null,
EndTime = null,
TypeConceptId = 45905770,
SourceValue = sourceValue
});
}
}
}
}
}
o.Add(new Observation(record)
{
Id = KeyMasterOffsetManager.GetKeyOffset(record.PersonId).ObservationId,
ValueAsNumber = decimalValue,
ValueAsString = decimalValue.HasValue ? valueAsString : value,
ConceptId = 0,
TypeConceptId = 44814721,
SourceValue = variable,
StartDate = new DateTime(year, 1, 1),
StartTime = new DateTime(year, 1, 1).ToString("HH:mm:ss", CultureInfo.InvariantCulture),
});
}
var r = BuildPerson(p);
var person = r.Key;
if (person == null)
{
Complete = true;
return(r.Value);
}
if (vo.Count > 0)
{
foreach (var entity in o)
{
entity.VisitOccurrenceId = vo[0].Id;
}
foreach (var entity in de)
{
entity.VisitOccurrenceId = vo[0].Id;
}
foreach (var entity in co)
{
entity.VisitOccurrenceId = vo[0].Id;
}
}
AddToChunk(person, null, op.ToArray(), new PayerPlanPeriod[0], de.ToArray(),
co.ToArray(), new ProcedureOccurrence[0], o.ToArray(), new Measurement[0],
vo.ToArray(), new VisitDetail[0], new Cohort[0], new DeviceExposure[0], new Note[0]);
Complete = true;
var pg = new PregnancyAlgorithm.PregnancyAlgorithm();
foreach (var pe in pg.GetPregnancyEpisodes(Vocabulary, person, op.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()))
{
pe.Id = KeyMasterOffsetManager.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 o)
{
this.Offset = o;
this.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 = KeyMasterOffsetManager.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 = KeyMasterOffsetManager.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.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 = KeyMasterOffsetManager.GetKeyOffset(pe.PersonId).ConditionEraId;
ChunkData.ConditionEra.Add(pe);
}
return(Attrition.None);
}
