Merge pull request #314 from answerdigital/feature/observation_source_value

Added observation_source_value mappings

Author: james-cockayne

OmopTransformer/SUS/APC/Observation/ICDDiagnosis/SusAPCSusDiagnosisObservation.cs

@@ -26,4 +26,7 @@ internal class SusAPCSusDiagnosisObservation : OmopObservation<SusAPCSusDiagnosi
 
     [Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.DiagnosisICD))]
     public override int? observation_source_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? observation_source_value { get; set; }
 }

OmopTransformer/SUS/APC/Observation/ProcedureObservations/SusAPCProcedureObservations.cs

@@ -26,4 +26,7 @@ internal class SusAPCProcedureObservations : OmopObservation<SusAPCProcedureObse
 
     [Transform(typeof(Opcs4Selector), nameof(Source.PrimaryProcedure))]
     public override int? observation_source_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.PrimaryProcedure))]
+    public override string? observation_source_value { get; set; }
 }

OmopTransformer/SUS/OP/Observation/ICDDiagnosis/SusOPICDDiagnosisObservation.cs

@@ -26,4 +26,7 @@ internal class SusOPICDDiagnosisObservation : OmopObservation<SusOPICDDiagnosisO
 
     [Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.DiagnosisICD))]
     public override int? observation_source_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? observation_source_value { get; set; }
 }

OmopTransformer/SUS/OP/Observation/ProcedureObservation/SusOPProcedureObservation.cs

@@ -26,4 +26,7 @@ internal class SusOPProcedureObservation : OmopObservation<SusOPProcedureObserva
 
     [Transform(typeof(Opcs4Selector), nameof(Source.PrimaryProcedure))]
     public override int? observation_source_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.PrimaryProcedure))]
+    public override string? observation_source_value { get; set; }
 }

docs/transformation-documentation/Observation_value_as_string.md

@@ -148,6 +148,32 @@ where NHSNumber is not null
 
 
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Observation%20table%20value_as_string%20field%20SUS%20APC%20Referral%20Received%20Date%20For%20Inpatients%20mapping){: .btn }
+### Sus APC Diagnosis Table
+* Value copied from `DiagnosisICD`
+
+* `DiagnosisICD` ICD10 diagnosis code [PRIMARY DIAGNOSIS (ICD)](https://www.datadictionary.nhs.uk/data_elements/primary_diagnosis__icd_.html)
+
+```sql
+select
+    distinct
+        d.DiagnosisICD,
+        apc.GeneratedRecordIdentifier,
+        apc.NHSNumber,
+        apc.CDSActivityDate
+from omop_staging.sus_ICDDiagnosis d
+    inner join omop_staging.sus_APC apc
+        on d.MessageId = apc.MessageId
+where apc.NHSNumber is not null
+order by
+	d.DiagnosisICD,
+    apc.GeneratedRecordIdentifier,
+    apc.NHSNumber,
+    apc.CDSActivityDate
+	
+```
+
+
+[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=OMOP%20Observation%20table%20value_as_string%20field%20Sus%20APC%20Diagnosis%20Table%20mapping){: .btn }
 ### SUS Inpatient Carer Support Indicator Observation
 * Value copied from `CarerSupportIndicator`
 

docs/transformation-documentation/SusAPCSusDiagnosisObservation.json

@@ -88,6 +88,24 @@
       "query": null,
       "lookup_table_markdown": null
     },
+    {
+      "name": "value_as_string",
+      "operation_description": "Value copied from `DiagnosisICD`",
+      "dataSource": [
+        {
+          "name": "DiagnosisICD",
+          "description": "ICD10 diagnosis code",
+          "origins": [
+            {
+              "origin": "PRIMARY DIAGNOSIS (ICD)",
+              "url": "https://www.datadictionary.nhs.uk/data_elements/primary_diagnosis__icd_.html"
+            }
+          ]
+        }
+      ],
+      "query": "\nselect\n    distinct\n        d.DiagnosisICD,\n        apc.GeneratedRecordIdentifier,\n        apc.NHSNumber,\n        apc.CDSActivityDate\nfrom omop_staging.sus_ICDDiagnosis d\n    inner join omop_staging.sus_APC apc\n        on d.MessageId = apc.MessageId\nwhere apc.NHSNumber is not null\norder by\n\td.DiagnosisICD,\n    apc.GeneratedRecordIdentifier,\n    apc.NHSNumber,\n    apc.CDSActivityDate\n\t",
+      "lookup_table_markdown": null
+    },
     {
       "name": "observation_source_concept_id",
       "operation_description": "Resolve ICD10 codes to standard or non standard OMOP concepts. If code cannot be mapped, map using the parent code.",