public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var obs = entity as Observation;
if (obs == null || obs.ValueAsNumber == 1)
{
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
}
break;
case "Measurement":
if (entity.TypeConceptId != 38000246)
{
var mes = entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
//var result = Vocabulary.Lookup(mes.SourceValue, "JMDC-ICD10-MapsToValue", DateTime.MinValue, false);
var result = Vocabulary.Lookup(mes.SourceValue, "JMDC-ICD10-MapsToValue", DateTime.MinValue);
int conceptId = 4181412;
if (result.Any() && result[0].ConceptId.HasValue && result[0].ConceptId > 0)
{
conceptId = result[0].ConceptId.Value;
}
if (mes.ValueAsConceptId == 0)
{
mes.ValueAsConceptId = conceptId;
}
ChunkData.AddData(mes);
}
break;
case "Meas Value":
ChunkData.AddData(entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
});
break;
case "Observation":
if (entity.TypeConceptId != 38000246)
{
var obser = entity as Observation ??
new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
//var result = Vocabulary.Lookup(obser.SourceValue, "JMDC-ICD10-MapsToValue", DateTime.MinValue, false);
var result = Vocabulary.Lookup(obser.SourceValue, "JMDC-ICD10-MapsToValue", DateTime.MinValue);
int conceptId = 4181412;
if (result.Any() && result[0].ConceptId.HasValue && result[0].ConceptId > 0)
{
conceptId = result[0].ConceptId.Value;
}
if (obser.ValueAsConceptId == 0)
{
obser.ValueAsConceptId = conceptId;
}
ChunkData.AddData(obser);
}
break;
case "Procedure":
var p = entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId)
.ProcedureOccurrenceId
};
ChunkData.AddData(p);
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
//HIX-823
if (domain == "Procedure" && entityDomain != "Procedure")
{
var po = (ProcedureOccurrence)entity;
po.ConceptId = 0;
ChunkData.AddData(po);
}
if (domain == "Observation" && entityDomain != "Observation")
{
var o = (Observation)entity;
o.ConceptId = 0;
ChunkData.AddData(o);
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
break;
case "Measurement":
ChunkData.AddData(entity as Measurement ?? new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
});
break;
case "Observation":
ChunkData.AddData(entity as Observation ?? new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
});
break;
case "Procedure":
ChunkData.AddData(entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId).ProcedureOccurrenceId
});
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var obs = entity as Observation;
if (obs == null || obs.ValueAsNumber == 1)
{
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId)
.ConditionOccurrenceId
};
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
}
break;
case "Measurement":
case "Meas Value":
var mes = entity as Measurement ?? new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
if (!string.IsNullOrEmpty(mes.SourceValue))
{
if (decimal.TryParse(mes.SourceValue, out var valueAsNumber))
{
mes.ValueAsNumber = valueAsNumber;
}
}
ChunkData.AddData(mes);
break;
case "Observation":
var o = entity as Observation ?? new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
if (!string.IsNullOrEmpty(o.SourceValue))
{
if (decimal.TryParse(o.SourceValue, out var valueAsNumber))
{
o.ValueAsNumber = valueAsNumber;
}
else if (string.IsNullOrEmpty(o.ValueAsString))
{
o.ValueAsString = o.SourceValue;
}
}
ChunkData.AddData(o);
break;
case "Procedure":
ChunkData.AddData(entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId)
.ProcedureOccurrenceId
});
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
//1.Look for day_sply_nbr.If this is not NULL, add the value in days to drug_exposure_start_date to get drug_exposure_end_date
//2.If there is a day_sply_nbr and a value in ptnt_mdctn_end_dte_tstmp, use the calculated value from step one as the drug_exposure_end_date
//3.If day_sply_nbr is NULL then use the ptnt_mdctn_end_dte_tstmp as the verbatim_end_date and drug_exposure_end_date
//4.If both day_sply_nbr is NULL and ptnt_mdctn_end_dte_tstmp is NULL then set the drug_exposure_end_date as the drug_exposure_start_date
if (drg.DaysSupply.HasValue && drg.DaysSupply > 0)
{
drg.EndDate = drg.StartDate.AddDays(drg.DaysSupply.Value);
}
else if (drg.VerbatimEndDate.HasValue)
{
drg.EndDate = drg.VerbatimEndDate;
}
else
{
drg.EndDate = drg.StartDate;
}
if (!string.IsNullOrEmpty(drg.Sig) && drg.Sig.Contains("~*~"))
{
drg.Sig = drg.Sig.Replace("~*~", "~x~");
}
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
if (!cond.EndDate.HasValue)
{
cond.EndDate = cond.StartDate;
}
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
break;
case "Measurement":
var mes = entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
ChunkData.AddData(mes);
break;
case "Meas Value":
var mv = entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
ChunkData.AddData(mv);
break;
case "Observation":
var o = entity as Observation ??
new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
ChunkData.AddData(o);
break;
case "Procedure":
var p = entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId).ProcedureOccurrenceId
};
ChunkData.AddData(p);
break;
case "Device":
var dev = entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
};
if (!dev.EndDate.HasValue)
{
dev.EndDate = dev.StartDate;
}
ChunkData.AddData(dev);
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
if (!drg.EndDate.HasValue)
{
drg.EndDate = drg.StartDate;
}
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var obs = entity as Observation;
if (obs == null || obs.ValueAsNumber == 1)
{
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
}
break;
case "Measurement":
var mes = entity as Measurement ??
new Measurement(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).MeasurementId
};
if (entity.AdditionalFields != null && entity.AdditionalFields.ContainsKey("test_result"))
{
mes.ValueSourceValue = entity.AdditionalFields["test_result"];
}
// HIX-1363
//if rslt_nbr is non-zero, take it for both fields, otherwise,
//use NULL for value_as_number and take rslt_txt for value_as_string.
if (mes.ValueAsNumber != null && mes.ValueAsNumber != 0)
{
mes.ValueSourceValue = mes.ValueAsNumber.ToString();
}
if (mes.TypeConceptId != 44786627 && mes.TypeConceptId != 44786629)
{
mes.TypeConceptId = 45754907;
}
ChunkData.AddData(mes);
break;
case "Meas Value":
var m = entity as Measurement ??
new Measurement(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).MeasurementId
};
if (entity.AdditionalFields != null && entity.AdditionalFields.ContainsKey("test_result"))
{
m.ValueSourceValue = entity.AdditionalFields["test_result"];
}
if (m.TypeConceptId != 44786627 && m.TypeConceptId != 44786629)
{
m.TypeConceptId = 45754907;
}
m.TypeConceptId = 45754907;
ChunkData.AddData(m);
break;
case "Observation":
var o = entity as Observation ??
new Observation(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).ObservationId
};
ChunkData.AddData(o);
break;
case "Procedure":
var proc = entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).ProcedureOccurrenceId
};
if (proc.TypeConceptId == 0)
{
proc.TypeConceptId = 38000275;
}
else if (proc.TypeConceptId == 44786627 || proc.TypeConceptId == 44786629)
{
proc.TypeConceptId = 42865906;
}
ChunkData.AddData(proc);
break;
case "Device":
var dev = entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).DeviceExposureId
};
ChunkData.AddData(dev);
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = KeyMasterOffsetManager.GetKeyOffset(entity.PersonId).DrugExposureId
};
if (drg.TypeConceptId == 0)
{
drg.TypeConceptId = 38000275;
}
if (!drg.EndDate.HasValue)
{
drg.EndDate = drg.StartDate;
}
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
//HIX-823
if (domain == "Procedure" && entityDomain != "Procedure")
{
var po = (ProcedureOccurrence)entity;
po.ConceptId = 0;
ChunkData.AddData(po);
}
if (domain == "Observation" && entityDomain != "Observation")
{
var o = (Observation)entity;
o.ConceptId = 0;
ChunkData.AddData(o);
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var obs = entity as Observation;
if (obs == null || obs.ValueAsNumber == 1)
{
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId)
.ConditionOccurrenceId
};
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
}
break;
case "Measurement":
var mes = entity as Measurement ?? new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
if (mes.ConceptId == 0 && _covid.Any(c => c == mes.SourceValue))
{
mes.ConceptId = 700360;
}
ChunkData.AddData(mes);
break;
case "Observation":
var o = entity as Observation ?? new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
ChunkData.AddData(o);
break;
case "Procedure":
ChunkData.AddData(entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId)
.ProcedureOccurrenceId
});
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
//Person < 12 years old with live birth. Removing condition_occurrence
if (cond.ConceptId == 4014295 && _personAge < 12)
{
continue;
}
//Male with live birth. Removing condition_occurrence
if (cond.ConceptId == 4014295 && _currentPerson.GenderConceptId == 8507)
{
continue;
}
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
break;
case "Measurement":
var mes = entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
mes.ValueAsConceptId = GetValueAsConceptId(mes, 4181412);
ChunkData.AddData(mes);
break;
case "Meas Value":
ChunkData.AddData(entity as Measurement ??
new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
});
break;
case "Observation":
var obser = entity as Observation ??
new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
obser.ValueAsConceptId = GetValueAsConceptId(obser, 45877994);
ChunkData.AddData(obser);
break;
case "Procedure":
ChunkData.AddData(entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id =
Offset.GetKeyOffset(entity.PersonId).ProcedureOccurrenceId
});
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
//HIX-823
if (domain == "Procedure" && entityDomain != "Procedure")
{
var po = (ProcedureOccurrence)entity;
po.ConceptId = 0;
ChunkData.AddData(po);
}
if (domain == "Observation" && entityDomain != "Observation")
{
var o = (Observation)entity;
o.ConceptId = 0;
ChunkData.AddData(o);
}
}
}
public override void AddToChunk(string domain, IEnumerable <IEntity> entities)
{
foreach (var entity in entities)
{
var entityDomain = GetDomain2(domain, entity.Domain);
switch (entityDomain)
{
case "Condition":
var cond = entity as ConditionOccurrence ??
new ConditionOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ConditionOccurrenceId
};
cond.TypeConceptId = 32020; //EHR encounter diagnosis
ConditionForEra.Add(cond);
ChunkData.AddData(cond);
break;
case "Measurement":
var mes = entity as Measurement ?? new Measurement(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).MeasurementId
};
mes.TypeConceptId = 44818702; //Lab result;
if (!string.IsNullOrEmpty(mes.SourceValue))
{
var result = Vocabulary.Lookup(mes.SourceValue, "Read_Code", mes.StartDate);
if (result.Any() &&
result.Count > 0 &&
result[0].SourceConceptId > 0
/*&& result[0].Domain == "Measurement"*/)
{
mes.SourceConceptId = result[0].SourceConceptId;
}
}
if (mes.ConceptId > 0)
{
if (string.Equals(mes.SourceValue, "4J3R200", StringComparison.Ordinal))
{
mes.ConceptId = 756065;
mes.ValueSourceValue = "Not Detected";
mes.ValueAsConceptId = 9190;
}
else if (string.Equals(mes.SourceValue, "4J3R100", StringComparison.Ordinal))
{
mes.ConceptId = 756065;
mes.ValueSourceValue = "Detected";
mes.ValueAsConceptId = 4126681;
}
else if (string.Equals(mes.SourceValue, "4J3R.00", StringComparison.Ordinal))
{
mes.ConceptId = 706179;
}
ChunkData.AddData(mes);
}
else
{
var o = new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
ChunkData.AddData(o);
}
break;
case "Observation":
var obs = entity as Observation ?? new Observation(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).ObservationId
};
obs.TypeConceptId = 38000280; //Observation recorded from EHR
var valueAsConceptId = GetValueAsConceptId(obs, obs.ValueAsString);
if (valueAsConceptId.HasValue)
{
obs.ValueAsConceptId = valueAsConceptId.Value;
}
ChunkData.AddData(obs);
break;
case "Procedure":
var proc = entity as ProcedureOccurrence ??
new ProcedureOccurrence(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId)
.ProcedureOccurrenceId
};
proc.TypeConceptId = 38000275; //EHR order list entry
ChunkData.AddData(proc);
break;
case "Device":
ChunkData.AddData(entity as DeviceExposure ??
new DeviceExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DeviceExposureId
});
break;
case "Drug":
var drg = entity as DrugExposure ??
new DrugExposure(entity)
{
Id = Offset.GetKeyOffset(entity.PersonId).DrugExposureId
};
drg.TypeConceptId = 38000177;
//Drug|CVX
if (entity.Domain != null && entity.Domain.EndsWith("CVX", StringComparison.OrdinalIgnoreCase))
{
drg.TypeConceptId = 38000179; // Physician administered drug (identified as procedure)
}
DrugForEra.Add(drg);
ChunkData.AddData(drg);
break;
}
}
}