Merge pull request #123 from OHDSI/value-as-conceptid-fix

Add support of the multiple VALUE_AS_CONCEPT_ID
OHDSI · Oct 9, 2024 · 4685c72 · 4685c72
2 parents 57cbee1 + 30975e6
commit 4685c72
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Showing 3 changed files with 30 additions and 38 deletions.
diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/EntityDefinition.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Definitions/EntityDefinition.cs
@@ -1,4 +1,5 @@
-using org.ohdsi.cdm.framework.common.Builder;
+using Force.DeepCloner;
+using org.ohdsi.cdm.framework.common.Builder;
 using org.ohdsi.cdm.framework.common.Extensions;
 using org.ohdsi.cdm.framework.common.Lookups;
 using org.ohdsi.cdm.framework.common.Omop;
@@ -131,7 +132,7 @@ public virtual IEnumerable<IEntity> GetConcepts(Concept concept, IDataRecord rea
                                 }
                             }
 
-                            yield return new Entity
+                            var entity =  new Entity
                             {
                                 IsUnique = IsUnique,
                                 PersonId = personId.Value,
@@ -150,17 +151,30 @@ public virtual IEnumerable<IEntity> GetConcepts(Concept concept, IDataRecord rea
                                 ValidEndDate = lookupValue.ValidEndDate,
                                 SourceConceptId = sourceConceptId,
                                 Domain = lookupValue.Domain,
-                                //SourceVocabularyId = lookupValue.SourceVocabularyId,
                                 VocabularySourceValue = lookupValue.SourceCode,
                                 Ingredients = ingredients,
-                                ValueAsConceptId = lookupValue.ValueAsConceptId,
+                                ValueAsConceptId = null,
                                 SourceConcepts = lookupValue.SourceConcepts.ToList(),
                             };
 
+
+                            if (lookupValue.ValueAsConceptIds == null || lookupValue.ValueAsConceptIds.Count == 0)
+                            {
+                                yield return entity;
+                            }
+                            else
+                            {
+                                foreach (var valueAsConceptId in lookupValue.ValueAsConceptIds)
+                                {
+                                    var ent = entity.DeepClone();
+                                    ent.ValueAsConceptId = valueAsConceptId;
+                                    yield return ent;
+                                }
+                            }
                         }
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Lookups/Lookup.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Lookups/Lookup.cs
@@ -136,33 +136,6 @@ public void Fill(AmazonS3Client client, string bucket, string prefix)
                             ValidEndDate = validEndDate
                         };
 
-                        //if (spliter.Results.Length > 5)
-                        //{
-                        //    //lv.SourceConceptId = IsNullOrEmpty(spliter.Results[6])
-                        //    //    ? 0
-                        //    //    : long.Parse(spliter.Results[6]);
-
-                        //    var sourceConceptId = IsNullOrEmpty(spliter.Results[6])
-                        //       ? 0
-                        //       : long.Parse(spliter.Results[6]);
-
-                        //    var sourceValidStartDate =  DateTime.MinValue;
-                        //    var sourceValidEndDate = DateTime.MaxValue;
-
-                        //    if (spliter.Results.Length > 6)
-                        //    {
-                        //        DateTime.TryParse(spliter.Results[7], out sourceValidStartDate);
-                        //        DateTime.TryParse(spliter.Results[8], out sourceValidEndDate);
-                        //    }
-
-                        //    lv.SourceConcepts.Add(new SourceConcepts 
-                        //    { 
-                        //        ConceptId = sourceConceptId, 
-                        //        ValidStartDate = sourceValidStartDate, 
-                        //        ValidEndDate = sourceValidEndDate 
-                        //    });
-                        //}
-
                         value = lv;
                         _lookup[sourceCode].Add(conceptId, value);
                     }
@@ -204,11 +177,16 @@ public void Fill(AmazonS3Client client, string bucket, string prefix)
                             value.Ingredients.Add(ingredient);
                         }
                     }
-                    
-                    if (spliter.Results.Length > 10)
+
+                     if (spliter.Results.Length > 10)
                     {
-                        if (!IsNullOrEmpty(spliter.Results[10]))
-                            value.ValueAsConceptId = long.Parse(spliter.Results[10]);
+
+                        if (!IsNullOrEmpty(spliter.Results[10]) &&
+                           long.TryParse(spliter.Results[10], out var valueAsConceptId))
+                        {
+                            value.ValueAsConceptIds ??= [];
+                            value.ValueAsConceptIds.Add(valueAsConceptId);
+                        }
                     }
                 }
             }
@@ -253,7 +231,7 @@ private IEnumerable<LookupValue> GetValues(string sourceCode, DateTime? eventDat
                     Ingredients = _lookup[sourceCode][conceptId].Ingredients,
                     ValidStartDate = _lookup[sourceCode][conceptId].ValidStartDate,
                     ValidEndDate = _lookup[sourceCode][conceptId].ValidEndDate,
-                    ValueAsConceptId = _lookup[sourceCode][conceptId].ValueAsConceptId,
+                    ValueAsConceptIds = _lookup[sourceCode][conceptId].ValueAsConceptIds,
                     //SourceValidStartDate = _lookup[sourceCode][conceptId].SourceValidStartDate,
                     //SourceValidEndDate = _lookup[sourceCode][conceptId].SourceValidEndDate,
                     SourceConcepts = _lookup[sourceCode][conceptId].SourceConcepts,

diff --git a/sources/Framework/org.ohdsi.cdm.framework/Common/Lookups/LookupValue.cs b/sources/Framework/org.ohdsi.cdm.framework/Common/Lookups/LookupValue.cs
@@ -34,7 +34,7 @@ public class LookupValue : IEquatable<LookupValue>
 
         public HashSet<SourceConcepts> SourceConcepts { get; set; } = [];
         public HashSet<long> Ingredients { get; set; }
-        public long? ValueAsConceptId { get; set; }
+        public HashSet<long> ValueAsConceptIds { get; set; }
 
         public bool Equals(LookupValue other)
         {