Merge pull request #119 from OHDSI/cost-definition

Cost definition
OHDSI · Sep 10, 2024 · b3d5e9f · b3d5e9f
2 parents 9e00212 + 4b709f8
commit b3d5e9f
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Showing 10 changed files with 225 additions and 7 deletions.
diff --git a/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/CDM/CdmPersonBuilder.cs b/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/CDM/CdmPersonBuilder.cs
@@ -228,6 +228,8 @@ public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
                 [.. conditionOccurrences], [.. procedureOccurrences], [.. observations], [.. measurements],
                 [.. visitOccurrences.Values], [.. visitDetails], null, [.. deviceExposure], null, null);
 
+            foreach (var c in CostRaw)
+                ChunkData.AddCostData(c);
 
             Complete = true;
 

diff --git a/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/CDM/Definitions/Cost.xml b/sources/Framework/org.ohdsi.cdm.framework.etl/Transformation/CDM/Definitions/Cost.xml
@@ -0,0 +1,71 @@
+<QueryDefinition>
+	<Query>
+		SELECT   cost_id
+		, cost_event_id
+		, cost_domain_id
+		, cost_type_concept_id
+		, currency_concept_id
+		, total_charge
+		, total_cost
+		, total_paid
+
+		, paid_by_payer
+		, paid_by_patient
+		, paid_patient_copay
+		, paid_patient_coinsurance
+		, paid_patient_deductible
+		, paid_by_primary
+		, paid_ingredient_cost
+		, paid_dispensing_fee
+
+		, payer_plan_period_id
+
+		, amount_allowed
+		, revenue_code_concept_id
+		, revenue_code_source_value
+		, drg_concept_id
+		, drg_source_value
+		, coalesce(po.person_id, o.person_id, d.person_id, dev.person_id, m.person_id, v.person_id) person_id
+		FROM {sc}.cost
+		left join {sc}.procedure_occurrence po on cost_domain_id = 'Procedure' and cost_event_id = po.procedure_occurrence_id
+		left join {sc}.observation o on cost_domain_id = 'Observation' and cost_event_id = o.observation_id
+		left join {sc}.drug_exposure d on cost_domain_id = 'Drug' and cost_event_id = d.drug_exposure_id
+		left join {sc}.device_exposure dev on cost_domain_id = 'Device' and cost_event_id = dev.device_exposure_id
+		left join {sc}.measurement m on cost_domain_id = 'Measurement' and cost_event_id = m.measurement_id
+		left join {sc}.visit_occurrence v on cost_domain_id = 'Visit' and cost_event_id = v.visit_occurrence_id
+		JOIN {ch_sc}._chunks ch ON ch.ChunkId = {0} AND coalesce(po.person_id, o.person_id, d.person_id, dev.person_id, m.person_id, v.person_id) = ch.PERSON_ID
+		order by 1
+	</Query>
+	<Costs>
+		<CostRawDefinition>
+			<PersonId>person_id</PersonId>
+
+			<Id>cost_id</Id>
+			<EventId>cost_event_id</EventId>
+			<DomainId>cost_domain_id</DomainId>
+			<TypeConceptId>cost_type_concept_id</TypeConceptId>
+			<CurrencyConceptId>currency_concept_id</CurrencyConceptId>
+			<TotalCharge>total_charge</TotalCharge>
+			<TotalCost>total_cost</TotalCost>
+			<TotalPaid>total_paid</TotalPaid>
+
+			<PaidByPayer>paid_by_payer</PaidByPayer>
+			<PaidByPatient>paid_by_patient</PaidByPatient>
+			<PaidPatientCopay>paid_patient_copay</PaidPatientCopay>
+			<PaidPatientCoinsurance>paid_patient_coinsurance</PaidPatientCoinsurance>
+			<PaidPatientDeductible>paid_patient_deductible</PaidPatientDeductible>
+			<PaidIngredientCost>paid_ingredient_cost</PaidIngredientCost>
+			<PaidDispensingFee>paid_dispensing_fee</PaidDispensingFee>
+
+			<PayerPlanPeriodId>payer_plan_period_id</PayerPlanPeriodId>
+
+			<AmountAllowed>amount_allowed</AmountAllowed>
+
+			<RevenueCodeConceptId>revenue_code_concept_id</RevenueCodeConceptId>
+			<RevenueCodeSourceValue>revenue_code_source_value</RevenueCodeSourceValue>
+
+			<DrgConceptId>drg_concept_id</DrgConceptId>
+			<DrgSourceValue>drg_source_value</DrgSourceValue>
+		</CostRawDefinition>
+	</Costs>
+</QueryDefinition>
diff --git a/sources/Framework/org.ohdsi.cdm.framework.etl/org.ohdsi.cdm.framework.etl.csproj b/sources/Framework/org.ohdsi.cdm.framework.etl/org.ohdsi.cdm.framework.etl.csproj
@@ -10,6 +10,7 @@
   <ItemGroup>
     <None Remove="Transformation\CDM\Batch.sql" />
     <None Remove="Transformation\CDM\Definitions\Condition_occurrence.xml" />
+    <None Remove="Transformation\CDM\Definitions\Cost.xml" />
     <None Remove="Transformation\CDM\Definitions\Death.xml" />
     <None Remove="Transformation\CDM\Definitions\Device_exposure.xml" />
     <None Remove="Transformation\CDM\Definitions\Drug_exposure.xml" />
@@ -303,6 +304,9 @@
     <EmbeddedResource Include="Transformation\CDM\Definitions\Condition_occurrence.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </EmbeddedResource>
+    <EmbeddedResource Include="Transformation\CDM\Definitions\Cost.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </EmbeddedResource>
     <EmbeddedResource Include="Transformation\CDM\Definitions\Death.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </EmbeddedResource>

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Base/IPersonBuilder.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Base/IPersonBuilder.cs
@@ -30,6 +30,8 @@ public interface IPersonBuilder
 
         void AddObservationPeriod(EraEntity data);
 
+        void AddCost(Cost data);
+
         //void Build(ChunkData chunkData);
         Attrition Build(ChunkData data, KeyMasterOffsetManager offset);
 

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Base/PersonBuilder.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Base/PersonBuilder.cs
@@ -35,6 +35,8 @@ public class PersonBuilder : IPersonBuilder
         protected List<DeviceExposure> DeviceExposureRaw = [];
         protected List<DeviceCost> DeviceCostRaw = [];
 
+        protected List<Cost> CostRaw = [];
+
         protected List<DrugExposure> DrugForEra = [];
         protected List<ConditionOccurrence> ConditionForEra = [];
         protected List<Note> NoteRecords = [];
@@ -226,6 +228,9 @@ public void Reset()
 
             EpisodeRecords.Clear();
             EpisodeRecords = null;
+
+            CostRaw.Clear();
+            CostRaw = null;
         }
 
         protected virtual bool AddCost(long eventId, Func<ICostV5, Cost> createCost, IEntity entity, ICostV5 entityCost)
@@ -239,6 +244,11 @@ protected virtual bool AddCost(long eventId, Func<ICostV5, Cost> createCost, IEn
             return ChunkData.AddCostData(cost);
         }
 
+        public void AddCost(Cost data)
+        {
+            CostRaw.Add(data);
+        }
+
         public ChunkData Result => ChunkData;
 
         public bool Complete { get; set; }
@@ -922,6 +932,9 @@ public virtual Attrition Build(ChunkData data, KeyMasterOffsetManager o)
             AddToChunk(person, death, observationPeriods, payerPlanPeriods, drugExposures,
                 conditionOccurrences, procedureOccurrences, observations, measurements,
                 [.. visitOccurrences.Values], visitDetails, cohort, deviceExposure, notes, episode);
+
+            foreach(var c in CostRaw)
+                ChunkData.AddCostData(c);
 
             Complete = true;
 

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/DataReaders/v5/v52/CostDataReader52.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/DataReaders/v5/v52/CostDataReader52.cs
@@ -27,17 +27,41 @@ public object GetValue(int i)
             switch (i)
             {
                 case 0:
+                    {
+                        if (_enumerator.Current.Id.HasValue)
+                            return _enumerator.Current.Id.Value;
 
-                    return _offset.GetId(_enumerator.Current.PersonId,
-                        _enumerator.Current.CostId); //TODO VisitCostOffset -> CostOffset
+                        return _offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.CostId);
+                    }
 
                 case 1:
+                    {
+                        if (_enumerator.Current.Domain == "Procedure" && !_offset
+                                .GetKeyOffset(_enumerator.Current.PersonId).ProcedureOccurrenceIdChanged)
+                            return _enumerator.Current.EventId;
 
-                    if (_enumerator.Current.Domain == "Visit" && !_offset
-                            .GetKeyOffset(_enumerator.Current.PersonId).VisitOccurrenceIdChanged)
-                        return _enumerator.Current.EventId;
+                        if (_enumerator.Current.Domain == "Observation" && !_offset
+                                .GetKeyOffset(_enumerator.Current.PersonId).ObservationIdChanged)
+                            return _enumerator.Current.EventId;
 
-                    return _offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.EventId);
+                        if (_enumerator.Current.Domain == "Drug" && !_offset
+                                .GetKeyOffset(_enumerator.Current.PersonId).DrugExposureIdChanged)
+                            return _enumerator.Current.EventId;
+
+                        if (_enumerator.Current.Domain == "Device" && !_offset
+                                .GetKeyOffset(_enumerator.Current.PersonId).DeviceExposureIdChanged)
+                            return _enumerator.Current.EventId;
+
+                        if (_enumerator.Current.Domain == "Measurement" && !_offset
+                                .GetKeyOffset(_enumerator.Current.PersonId).MeasurementIdChanged)
+                            return _enumerator.Current.EventId;
+
+                        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 2:
                     return _enumerator.Current.Domain;
 

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/CostRawDefinition.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/CostRawDefinition.cs
@@ -0,0 +1,82 @@
+using org.ohdsi.cdm.framework.common.Builder;
+using org.ohdsi.cdm.framework.common.Extensions;
+using org.ohdsi.cdm.framework.common.Omop;
+using System.Data;
+
+namespace org.ohdsi.cdm.framework.common.Definitions
+{
+    public class CostRawDefinition : EntityDefinition
+    {
+        public string TypeConceptId { get; set; }
+
+        public string EventId { get; set; }
+        public string DomainId { get; set; }
+        public string CurrencyConceptId { get; set; }
+        public string TotalCharge { get; set; }
+        public string TotalCost { get; set; }
+        public string TotalPaid { get; set; }
+
+
+        public string PaidByPayer { get; set; }
+        public string PaidByPatient { get; set; }
+        public string PaidPatientCopay { get; set; }
+        public string PaidPatientCoinsurance { get; set; }
+        public string PaidPatientDeductible { get; set; }
+        public string PaidIngredientCost { get; set; }
+        public string PaidDispensingFee { get; set; }
+
+        public string PayerPlanPeriodId { get; set; }
+
+        public string AmountAllowed { get; set; }
+
+        public string RevenueCodeConceptId { get; set; }
+        public string RevenueCodeSourceValue { get; set; }
+
+        public string DrgConceptId { get; set; }
+        public string DrgSourceValue { get; set; }
+
+
+        public IEnumerable<Cost> GetCost(Concept concept, IDataRecord reader,
+           KeyMasterOffsetManager offset)
+        {
+            var presonId = reader.GetLong(PersonId);
+            yield return new Cost(presonId.Value)
+            {
+                Id = reader.GetLong(Id),
+
+                PersonId = presonId.Value,
+                TypeId = reader.GetLong(TypeConceptId),
+
+                EventId = reader.GetLong(EventId) ?? 0,
+                Domain = reader.GetString(DomainId),
+                CurrencyConceptId = reader.GetLong(CurrencyConceptId) ?? 0,
+                TotalCharge = reader.GetDecimal(TotalCharge),
+                TotalCost = reader.GetDecimal(TotalCost),
+                TotalPaid = reader.GetDecimal(TotalPaid),
+
+                PaidByPayer = reader.GetDecimal(PaidByPayer),
+                PaidByPatient = reader.GetDecimal(PaidByPatient),
+                PaidPatientCopay = reader.GetDecimal(PaidPatientCopay),
+                PaidPatientCoinsurance = reader.GetDecimal(PaidPatientCoinsurance),
+                PaidPatientDeductible = reader.GetDecimal(PaidPatientDeductible),
+                PaidIngredientCost = reader.GetDecimal(PaidIngredientCost),
+                PaidDispensingFee = reader.GetDecimal(PaidDispensingFee),
+
+                PayerPlanPeriodId = reader.GetLong(PayerPlanPeriodId),
+
+                AmountAllowed = reader.GetDecimal(AmountAllowed),
+
+                RevenueCodeConceptId = reader.GetLong(RevenueCodeConceptId),
+                RevenueCodeSourceValue = reader.GetString(RevenueCodeSourceValue),
+
+                DrgConceptId = reader.GetLong(DrgConceptId),
+                DrgSourceValue = reader.GetString(DrgSourceValue)
+            };
+        }
+
+        public override IEnumerable<IEntity> GetConcepts(Concept concept, IDataRecord reader, KeyMasterOffsetManager offset)
+        {
+            throw new NotImplementedException("CostDefinitionRaw.GetConcepts()");
+        }
+    }
+}
diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/QueryDefinition.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/QueryDefinition.cs
@@ -92,6 +92,8 @@ public class QueryDefinition
         public EpisodeEventDefinition[] EpisodeEvents { get; set; }
         public ObservationPeriodDefinition[] ObservationPeriods { get; set; }
 
+        public CostRawDefinition[] Costs { get; set; }
+
         private static readonly string[] separator = [","];
 
         public void RowProcessed()
@@ -261,6 +263,11 @@ public string GetPersonIdFieldName()
                 return ObservationPeriods[0].PersonId;
             }
 
+            if (Costs != null && Costs.Length != 0)
+            {
+                return Costs[0].PersonId;
+            }
+
             throw new Exception("Cant find PersonId FieldName " + this.FileName);
         }
     }

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Omop/Cost.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Omop/Cost.cs
@@ -2,9 +2,12 @@
 {
     public class Cost(long personId)
     {
+        public long? Id { get; set; }
+        public long CostId { get; set; }
+
         public long PersonId { get; set; } = personId;
         public string Domain { get; set; }
-        public long CostId { get; set; }
+
         public long EventId { get; set; }
 
         public long? TypeId { get; set; }

diff --git a/sources/Presentation/org.ohdsi.cdm.presentation.lambdabuilder/Base/LambdaChunkPart.cs b/sources/Presentation/org.ohdsi.cdm.presentation.lambdabuilder/Base/LambdaChunkPart.cs
@@ -322,6 +322,7 @@ private void Watchdog_Elapsed(object sender, System.Timers.ElapsedEventArgs e)
                             AddEntity(qd, qd.Note, reader, recordGuid, personIdsToSave);
                             AddEntity(qd, qd.Episodes, reader, recordGuid, personIdsToSave);
                             AddEntity(qd, qd.ObservationPeriods, reader, recordGuid, personIdsToSave);
+                            AddEntity(qd, qd.Costs, reader, recordGuid, personIdsToSave);
 
                             if (reader.Paused)
                                 break;
@@ -650,6 +651,15 @@ private void AddEntity(QueryDefinition queryDefinition, IEnumerable<EntityDefini
                             _personBuilders[op.PersonId].Value.AddObservationPeriod(op);
                         }
                     }
+                    else if (d is CostRawDefinition)
+                    {
+                        foreach (var c in ((CostRawDefinition)d).GetCost(conceptDef, reader, _offsetManager))
+                        {
+                            if (c == null) continue;
+
+                            _personBuilders[c.PersonId].Value.AddCost(c);
+                        }
+                    }
                     else
                     {
                         foreach (var entity in d.GetConcepts(conceptDef, reader, _offsetManager))