Merge pull request #161 from OHDSI/cdm-to-cdm-add-vocab

Cdm to cdm add vocab
OHDSI · Feb 19, 2025 · b5146c1 · b5146c1
2 parents f8f032a + d807e97
commit b5146c1
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Showing 3 changed files with 36 additions and 15 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
@@ -133,7 +133,7 @@ public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
                 visitOccurrences.Add(visitOccurrence.Id, visitOccurrence);
             }
 
-            var visitDetails = new List<VisitDetail>();
+            var visitDetails = new Dictionary<long, VisitDetail>();
 
             foreach (var vd in VisitDetailsRaw)
             {
@@ -143,7 +143,7 @@ public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
                     continue;
                 }
 
-                visitDetails.Add(vd);
+                visitDetails.Add(vd.Id, vd);
             }
 
             foreach (var de in DrugExposuresRaw)
@@ -182,12 +182,12 @@ public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
                     de.Domain = "Device";
             }
 
-            TryToRemap(DrugExposuresRaw);
-            TryToRemap(ConditionOccurrencesRaw);
-            TryToRemap(ProcedureOccurrencesRaw);
-            TryToRemap(ObservationsRaw);
-            TryToRemap(MeasurementsRaw);
-            TryToRemap(DeviceExposureRaw);
+            TryToRemap(DrugExposuresRaw, visitOccurrences, visitDetails);
+            TryToRemap(ConditionOccurrencesRaw, visitOccurrences, visitDetails);
+            TryToRemap(ProcedureOccurrencesRaw, visitOccurrences, visitDetails);
+            TryToRemap(ObservationsRaw, visitOccurrences, visitDetails);
+            TryToRemap(MeasurementsRaw, visitOccurrences, visitDetails);
+            TryToRemap(DeviceExposureRaw, visitOccurrences, visitDetails);
 
             var newEntities = new List<IEntity>();
 
@@ -226,7 +226,7 @@ public override Attrition Build(ChunkData data, KeyMasterOffsetManager o)
             // push built entities to ChunkBuilder for further save to CDM database
             AddToChunk(person, death, [.. observationPeriods], payerPlanPeriods, [.. drugExposures],
                 [.. conditionOccurrences], [.. procedureOccurrences], [.. observations], [.. measurements],
-                [.. visitOccurrences.Values], [.. visitDetails], null, [.. deviceExposure], null, null);
+                [.. visitOccurrences.Values], [.. visitDetails.Values], null, [.. deviceExposure], null, null);
 
             foreach (var c in CostRaw)
                 ChunkData.AddCostData(c);
@@ -398,11 +398,16 @@ protected IEnumerable<T> GetNewMap<T>(IEnumerable<T> entities, List<IEntity> new
             }
         }
 
-        private void TryToRemap(IEnumerable<IEntity> records)
+        private void TryToRemap(IEnumerable<IEntity> records, Dictionary<long, VisitOccurrence> visits, Dictionary<long, VisitDetail> visitDetails)
         {
             foreach (var record in records)
             {
-                if(record.VisitOccurrenceId.HasValue && _removedVisitIds.ContainsKey(record.VisitOccurrenceId.Value))
+                if (record.VisitOccurrenceId.HasValue && _removedVisitIds.ContainsKey(record.VisitOccurrenceId.Value))
+                {
+                    record.VisitOccurrenceId = null;
+                }
+
+                if (record.VisitOccurrenceId.HasValue && !visits.ContainsKey(record.VisitOccurrenceId.Value))
                 {
                     record.VisitOccurrenceId = null;
                 }
@@ -412,7 +417,12 @@ private void TryToRemap(IEnumerable<IEntity> records)
                     record.VisitDetailId = null;
                 }
 
-               UpdateLookup(record);
+                if (record.VisitDetailId.HasValue && !visitDetails.ContainsKey(record.VisitDetailId.Value))
+                {
+                    record.VisitDetailId = null;
+                }
+
+                UpdateLookup(record);
             }
         }
 
@@ -436,6 +446,9 @@ private void UpdateLookup(IEntity e)
                     case "icd10pcs":
                         lookupName = "icd10pcs";
                         break;
+                    case "icd10":
+                        lookupName = "icd10";
+                        break;
                     case "icd9cm":
                         lookupName = "icd9cm";
                         break;

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
@@ -105,8 +105,15 @@ public object GetValue(int i)
                     return _enumerator.Current.PaidDispensingFee.Round();
 
                 case 16:
-                    return (long?)_offset.GetId(_enumerator.Current.PersonId,
-                        _enumerator.Current.PayerPlanPeriodId.Value);
+                    if (_enumerator.Current.PayerPlanPeriodId.HasValue)
+                    {
+                        if (_offset.GetKeyOffset(_enumerator.Current.PersonId).PayerPlanPeriodIdChanged)
+                            return _offset.GetId(_enumerator.Current.PersonId, _enumerator.Current.PayerPlanPeriodId.Value);
+                        else
+                            return _enumerator.Current.PayerPlanPeriodId;
+                    }
+
+                    return null;
 
                 case 17:
                     return _enumerator.Current.AmountAllowed.Round();

diff --git a/sources/Presentation/org.ohdsi.cdm.presentation.lambdabuilder/Vocabulary.cs b/sources/Presentation/org.ohdsi.cdm.presentation.lambdabuilder/Vocabulary.cs
@@ -169,7 +169,7 @@ public void Fill(bool forLookup, bool readFromS3)
                 _lookups.Add(o.Key.Split('/')[3].Replace(".txt.gz", ""), lookup);
             }
 
-            if (Vendor is framework.etl.Transformation.CDM.CdmPersonBuilder.CdmVendor)
+            if (Vendor.Name == "CDM")
             {
                 var getObjectRequest = new GetObjectRequest
                 {
@@ -197,6 +197,7 @@ public void Fill(bool forLookup, bool readFromS3)
                 }
 
                 _conceptIdToSourceVocabularyId.TrimExcess();
+                Console.WriteLine("_conceptIdToSourceVocabularyId: " + _conceptIdToSourceVocabularyId.Keys.Count);
             }
         }