public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager keyOffset)
{
var visitDetails = base.GetConcepts(concept, reader, keyOffset).ToList();
if (visitDetails.Count > 0)
{
int? dischargeToConceptId = null;
string dischargeToSourceValue = null;
if (Concepts != null)
{
var dischargeConcept = Concepts.FirstOrDefault(c => c.Name == "DischargeToConceptId");
if (dischargeConcept != null)
{
var dischargeConcepts = base.GetConcepts(dischargeConcept, reader, null).ToList();
dischargeToSourceValue = reader.GetString(dischargeConcept.Fields[0].Key);
if (dischargeConcepts.Count > 0)
{
dischargeToConceptId = dischargeConcepts[0].ConceptId;
dischargeToSourceValue = dischargeConcepts[0].SourceValue;
}
}
}
else
{
dischargeToConceptId = reader.GetInt(DischargeToConceptId);
dischargeToSourceValue = reader.GetString(DischargeToSourceValue);
}
int? admittingSourceConceptId = null;
string admittingSourceValue = null;
if (Concepts != null)
{
var admittingConcept = Concepts.FirstOrDefault(c => c.Name == "AdmittedFromConceptId");
if (admittingConcept != null)
{
var admittingConcepts = base.GetConcepts(admittingConcept, reader, null).ToList();
admittingSourceValue = reader.GetString(admittingConcept.Fields[0].Key);
if (admittingConcepts.Count > 0)
{
admittingSourceConceptId = admittingConcepts[0].ConceptId;
admittingSourceValue = admittingConcepts[0].SourceValue;
}
}
}
else
{
admittingSourceConceptId = reader.GetInt(AdmittingSourceConceptId);
admittingSourceValue = reader.GetString(AdmittingSourceValue);
}
var id = reader.GetLong(Id);
var visitDetail = new VisitDetail((Entity)visitDetails[0])
{
CareSiteId = reader.GetLong(CareSiteId) ?? 0,
AdmittingSourceConceptId = admittingSourceConceptId ?? 0,
AdmittingSourceValue = admittingSourceValue,
DischargeToConceptId = dischargeToConceptId ?? 0,
DischargeToSourceValue = dischargeToSourceValue,
PrecedingVisitDetailId = reader.GetInt(PrecedingVisitDetailId)
};
if (id.HasValue)
{
visitDetail.Id = id.Value;
}
else
{
visitDetail.IdUndefined = true;
}
yield return(visitDetail);
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager keyOffset)
{
var locationSourceValue = reader.GetString(Location);
long?locationId = null;
if (!string.IsNullOrEmpty(Location))
{
locationId = Entity.GetId(locationSourceValue);
}
var genderSource = reader.GetString(Gender);
var genderConceptId = Vocabulary.LookupGender(genderSource);
var personId = reader.GetLong(PersonId);
if (personId.HasValue)
{
Dictionary <string, string> additionalFields = null;
if (AdditionalFields != null)
{
additionalFields =
new Dictionary <string, string>(AdditionalFields.Length, StringComparer.OrdinalIgnoreCase);
foreach (var additionalField in AdditionalFields)
{
additionalFields.Add(additionalField, reader.GetString(additionalField));
}
}
var startDate = reader.GetDateTime(StartDate);
var endDate = reader.GetDateTime(EndDate);
var startTime = reader.GetTime(StartTime) ??
startDate.TimeOfDay;
var endTime = reader.GetTime(EndTime) ?? endDate.TimeOfDay;
DateTime?timeOfBirth = null;
var tob = reader.GetDateTime(TimeOfBirth);
if (tob > DateTime.MinValue)
{
timeOfBirth = tob;
}
var deathDatetime = reader.GetDateTime(DeathDatetime);
yield return(new Person
{
ObservationPeriodGap = reader.GetInt(ObservationPeriodGap) ?? 32,
AdditionalFields = additionalFields,
PersonId = personId.Value,
StartDate = startDate,
EndDate = endDate,
PersonSourceValue = reader.GetString(PersonSourceValue),
GenderSourceValue = genderSource,
GenderConceptId = genderConceptId ?? 0,
LocationId = locationId,
YearOfBirth = reader.GetInt(YearOfBirth),
MonthOfBirth = reader.GetInt(MonthOfBirth),
DayOfBirth = reader.GetInt(DayOfBirth),
TimeOfDeath = deathDatetime == DateTime.MinValue ? (DateTime?)null : deathDatetime,
LocationSourceValue = locationSourceValue,
CareSiteId = reader.GetLong(CareSiteId),
EthnicitySourceValue = reader.GetString(Ethnicity),
EthnicityConceptId = reader.GetInt(EthnicityConceptId) ?? 0,
RaceSourceValue = reader.GetString(Race),
RaceConceptId = reader.GetInt(RaceConceptId) ?? 0,
ProviderId = reader.GetLong(ProviderId),
TimeOfBirth = timeOfBirth,
GenderSourceConceptId = reader.GetInt(GenderSourceConceptId) ?? 0, // CCAE
RaceSourceConceptId = reader.GetInt(RaceSourceConceptId) ?? 0,
EthnicitySourceConceptId = reader.GetInt(EthnicitySourceConceptId) ?? 0,
TypeConceptId = reader.GetInt(PeriodTypeConceptId),
PotentialChildId = reader.GetLong(PotentialChildId),
PotentialChildBirthDate = reader.GetDateTime(PotentialChildBirthDate)
});
}
}
public virtual IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
var personId = reader.GetLong(PersonId);
if (personId.HasValue)
{
var startDate = reader.GetDateTime(StartDate);
var endDate = startDate;
if (!string.IsNullOrEmpty(EndDate))
{
endDate = reader.GetDateTime(EndDate);
}
Dictionary <string, string> additionalFields = null;
if (AdditionalFields != null)
{
additionalFields =
new Dictionary <string, string>(AdditionalFields.Length, StringComparer.OrdinalIgnoreCase);
foreach (var additionalField in AdditionalFields)
{
//additionalFields.Add(String.Intern(additionalField.ToLower()), reader.GetString(additionalField));
additionalFields.Add(additionalField, reader.GetString(additionalField));
}
}
if (concept != null && concept.Fields != null)
{
foreach (var field in concept.Fields)
{
var sourceValue = field.DefaultSource;
if (string.IsNullOrEmpty(sourceValue))
{
sourceValue = reader.GetString(field.Key);
}
if (!field.IsNullable && string.IsNullOrEmpty(sourceValue) && field.DefaultConceptId == null &&
field.ConceptId == null)
{
continue;
}
// Used when: field.Key used for conceptId mapping and
// field.SourceKey used for SourceValue (by default field.Key and field.SourceKey are identical)
if (!string.IsNullOrEmpty(field.SourceKey))
{
sourceValue = reader.GetString(field.SourceKey);
}
foreach (var lookupValue in concept.GetConceptIdValues(Vocabulary, field, reader))
{
var cId = lookupValue.ConceptId;
if (!cId.HasValue && field.DefaultConceptId.HasValue)
{
cId = field.DefaultConceptId;
}
if (!concept.IdRequired || cId.HasValue)
{
var providerIdKey = reader.GetString(ProviderIdKey);
if (!string.IsNullOrEmpty(providerIdKey))
{
providerIdKey = providerIdKey.TrimStart('0');
}
List <int> ingredients = null;
if (lookupValue.Ingredients != null)
{
ingredients = new List <int>(lookupValue.Ingredients.Count);
ingredients.AddRange(lookupValue.Ingredients);
}
if (!string.IsNullOrEmpty(StartTime))
{
if (DateTime.TryParse(reader.GetString(StartTime), out var dt))
{
startDate = startDate + dt.TimeOfDay;
}
}
if (endDate != DateTime.MinValue && !string.IsNullOrEmpty(EndTime))
{
if (DateTime.TryParse(reader.GetString(EndTime), out var dt))
{
endDate = endDate + dt.TimeOfDay;
}
}
yield return(new Entity
{
IsUnique = IsUnique,
PersonId = personId.Value,
SourceValue = sourceValue,
ConceptId = cId ?? 0,
TypeConceptId = concept.GetTypeId(field, reader) ?? 0,
ConceptIdKey = reader.GetString(field.Key),
StartDate = startDate,
EndDate = endDate == DateTime.MinValue ? (DateTime?)null : endDate,
ProviderId = reader.GetLong(ProviderId),
ProviderKey = providerIdKey,
VisitOccurrenceId = reader.GetLong(VisitOccurrenceId),
VisitDetailId = reader.GetLong(VisitDetailId),
AdditionalFields = additionalFields,
ValidStartDate = lookupValue.ValidStartDate,
ValidEndDate = lookupValue.ValidEndDate,
SourceConceptId = lookupValue.SourceConceptId,
Domain = lookupValue.Domain,
//SourceVocabularyId = lookupValue.SourceVocabularyId,
VocabularySourceValue = lookupValue.SourceCode,
Ingredients = ingredients
});
}
}
}
}
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager keyOffset)
{
var personId = reader.GetLong(PersonId);
var startDate = reader.GetDateTime(StartDate);
var endDate = reader.GetDateTime(EndDate);
long?id = 0;
if (!string.IsNullOrEmpty(Id))
{
id = reader.GetLong(Id);
}
if (personId.HasValue)
{
Dictionary <string, string> additionalFields = null;
if (AdditionalFields != null)
{
additionalFields =
new Dictionary <string, string>(AdditionalFields.Length, StringComparer.OrdinalIgnoreCase);
foreach (var additionalField in AdditionalFields)
{
additionalFields.Add(additionalField, reader.GetString(additionalField));
}
}
var payerSourceValue = reader.GetString(PayerSource);
if (string.IsNullOrWhiteSpace(payerSourceValue))
{
payerSourceValue = null;
}
var planSource = reader.GetString(PlanSource);
if (string.IsNullOrWhiteSpace(planSource))
{
planSource = null;
}
int payerConceptId = 0;
int payerSourceConceptId = 0;
int planConceptId = 0;
int planSourceConceptId = 0;
int sponsorConceptId = 0;
int sponsorSourceConceptId = 0;
string sponsorSource = null;
int stopReasonConceptId = 0;
int stopReasonSourceConceptId = 0;
string stopReasonSource = null;
if (Concepts != null) // payer_concept_id
{
var payerConcept = Concepts.FirstOrDefault(c => c.Name == "PayerConceptId");
if (payerConcept != null)
{
var payerConcepts = base.GetConcepts(payerConcept, reader, null).ToList();
payerSourceValue = reader.GetString(payerConcept.Fields[0].Key);
if (payerConcepts.Count > 0)
{
payerConceptId = payerConcepts[0].ConceptId;
payerSourceConceptId = payerConcepts[0].SourceConceptId;
}
}
var planConcept = Concepts.FirstOrDefault(c => c.Name == "PlanConceptId");
if (planConcept != null)
{
var planConcepts = base.GetConcepts(planConcept, reader, null).ToList();
planSource = reader.GetString(planConcept.Fields[0].Key);
if (planConcepts.Count > 0)
{
planConceptId = planConcepts[0].ConceptId;
planSourceConceptId = planConcepts[0].SourceConceptId;
}
}
var sponsorConcept = Concepts.FirstOrDefault(c => c.Name == "SponsorConceptId");
if (sponsorConcept != null)
{
var sponsorConcepts = base.GetConcepts(sponsorConcept, reader, null).ToList();
sponsorSource = reader.GetString(sponsorConcept.Fields[0].Key);
if (sponsorConcepts.Count > 0)
{
sponsorConceptId = sponsorConcepts[0].ConceptId;
sponsorSourceConceptId = sponsorConcepts[0].SourceConceptId;
}
}
var stopReasonConcept = Concepts.FirstOrDefault(c => c.Name == "StopReasonConceptId");
if (stopReasonConcept != null)
{
var stopReasonConcepts = base.GetConcepts(stopReasonConcept, reader, null).ToList();
stopReasonSource = reader.GetString(stopReasonConcept.Fields[0].Key);
if (stopReasonConcepts.Count > 0)
{
stopReasonConceptId = stopReasonConcepts[0].ConceptId;
stopReasonSourceConceptId = stopReasonConcepts[0].SourceConceptId;
}
}
}
yield return(new PayerPlanPeriod
{
Id = id ?? 0,
PersonId = personId.Value,
StartDate = startDate,
EndDate = endDate,
PayerConceptId = payerConceptId,
PayerSourceConceptId = payerSourceConceptId,
PayerSourceValue = payerSourceValue,
PlanConceptId = planConceptId,
PlanSourceConceptId = planSourceConceptId,
PlanSourceValue = planSource,
SponsorConceptId = sponsorConceptId,
SponsorSourceConceptId = sponsorSourceConceptId,
SponsorSourceValue = sponsorSource,
StopReasonConceptId = stopReasonConceptId,
StopReasonSourceConceptId = stopReasonSourceConceptId,
StopReasonSourceValue = stopReasonSource,
FamilySourceValue = reader.GetString(FamilySource),
VisitOccurrenceId = reader.GetLong(VisitOccurrenceId),
AdditionalFields = additionalFields
});
}
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader,
KeyMasterOffsetManager keyOffset)
{
int? genderConceptId = 0;
string genderSource = null;
int? specialtyConceptId = 0;
int? specialtySourceConceptId = 0;
string specialtySource = null;
if (Concepts != null)
{
var genderConcept = Concepts.FirstOrDefault(c => c.Name == "GenderConceptId");
if (genderConcept != null)
{
var genderConcepts = genderConcept.GetConceptIdValues(Vocabulary, genderConcept.Fields[0], reader);
genderSource = reader.GetString(genderConcept.Fields[0].Key);
if (genderConcepts.Count > 0)
{
genderConceptId = genderConcepts.Min(c => c.ConceptId);
genderSource = genderConcepts.Min(c => c.SourceCode);
if (string.IsNullOrEmpty(genderSource))
{
genderSource = reader.GetString(genderConcept.Fields[0].Key);
}
if (string.IsNullOrEmpty(genderSource))
{
genderSource = reader.GetString(genderConcept.Fields[0].SourceKey);
}
}
}
var specialtyConcept = Concepts.FirstOrDefault(c => c.Name == "SpecialtyConceptId");
if (specialtyConcept != null)
{
var specialtyConcepts = specialtyConcept.GetConceptIdValues(Vocabulary, specialtyConcept.Fields[0], reader);
specialtySource = reader.GetString(specialtyConcept.Fields[0].Key);
if (specialtyConcepts.Count > 0)
{
specialtyConceptId = specialtyConcepts.Min(c => c.ConceptId);
specialtySourceConceptId = specialtyConcepts.Min(c => c.SourceConceptId);
specialtySource = specialtyConcepts.Min(c => c.SourceCode);
if (string.IsNullOrEmpty(specialtySource))
{
specialtySource = reader.GetString(specialtyConcept.Fields[0].Key);
}
if (string.IsNullOrEmpty(specialtySource))
{
specialtySource = reader.GetString(specialtyConcept.Fields[0].SourceKey);
}
}
}
}
var prov = new Provider
{
CareSiteId = reader.GetLong(CareSiteId) ?? 0,
ConceptId = specialtyConceptId ?? 0,
ProviderSourceValue = reader.GetString(ProviderSourceValue),
SourceValue = specialtySource,
Name = reader.GetString(Name),
YearOfBirth = reader.GetInt(YearOfBirth),
GenderConceptId = genderConceptId,
GenderSourceValue = reader.GetString(GenderSourceValue),
Npi = reader.GetString(NPI),
Dea = reader.GetString(DEA),
GenderSourceConceptId = reader.GetInt(GenderSourceConceptId) ?? 0,
SpecialtySourceConceptId = specialtySourceConceptId ?? 0
};
prov.Id = string.IsNullOrEmpty(Id) ? Entity.GetId(prov.GetKey()) : reader.GetLong(Id).Value;
yield return(prov);
}
public override IEnumerable <IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
{
DateTime?endDate = null;
int routeConceptId = 0;
string routeSourceValue = null;
if (Concepts.Length == 2)
{
var routeConcepts = base.GetConcepts(Concepts[1], reader, null).ToList();
routeSourceValue = reader.GetString(Concepts[1].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 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;
int?operatorConceptId = null;
if (Concepts != null)
{
var valueConcept = Concepts.FirstOrDefault(c => c.Name == "ValueAsConceptId");
if (valueConcept != null)
{
var valueConcepts = base.GetConcepts(valueConcept, reader, null).ToList();
if (valueConcepts.Count > 0)
{
valueAsConceptId = valueConcepts[0].ConceptId;
}
}
var operatorConcept = Concepts.FirstOrDefault(c => c.Name == "OperatorConceptId");
if (operatorConcept != null)
{
var operatorConcepts = base.GetConcepts(operatorConcept, reader, null).ToList();
if (operatorConcepts.Count > 0)
{
operatorConceptId = operatorConcepts[0].ConceptId;
}
}
}
else
{
if (operatorConceptId == null)
{
operatorConceptId = reader.GetInt(OperatorConceptId);
}
if (valueAsConceptId == null)
{
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 = 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)
});
}
}
