Merge pull request #298 from answerdigital/new-regression-fixes

New regression fixes

Author: khayamAmin

OmopTransformer/RTDS/ProcedureOccurrence/RtdsProcedureOccurrence.xml

@@ -22,7 +22,7 @@ with records as (
 		r.*
 	from records r
 )
-select
+select distinct
 	PatientId,
 	ProcedureCode,
 	Start_date as event_start_date,

OmopTransformer/RTDS/RtdsTransformer.cs

@@ -93,12 +93,6 @@ await Transform<RtdsVisitOccurrenceRecord, RtdsVisitOccurrence>(
          runId,
          cancellationToken);
 
-        await Transform<RtdsVisitOccurrenceRecord, RtdsVisitOccurrence>(
-        _visitOccurrenceRecorder.InsertUpdateVisitOccurrence,
-        "Rtds Visit Occurrence",
-        runId,
-        cancellationToken);
-
         await Transform<RtdsProviderRecord, RtdsProvider>(
         _providerRecorder.InsertUpdateProvider,
         "Rtds Provider",

OmopTransformer/RTDS/VisitOccurrence/RtdsVisitOccurrence.cs

@@ -4,15 +4,9 @@
 
 namespace OmopTransformer.RTDS.VisitOccurrence;
 
-[Notes(
-    "Assumptions",
-    "* `Emergency` covers a visit to A&E within the given Hospital Provider, and hence covers Admission Code 21 and 24 only",
-    "* `Location Class` ID 24 is a Consultant Clinic within the Health Care Provider.",
-    "* `Patient Classification` ID 1 is the only entry that covers 24 hours or more with the use of a bed, and whilst others may be a day/night only, they will be discounted because they are less than 24 hours. Also, maternity is also not taken as an `Inpatient` visit.",
-    "* No calculations to be made between Start and end visit date to try to calculate 24 hours, but instead the `Patient Classification` will be sufficient")]
 internal class RtdsVisitOccurrence : OmopVisitOccurrence<RtdsVisitOccurrenceRecord>
 {
-    [CopyValue(nameof(Source.PatientId))]
+    [CopyValue(nameof(Source.NhsNumber))]
     public override string? NhsNumber { get; set; }
 
     [Transform(typeof(DateConverter), nameof(Source.event_start_date))]

OmopTransformer/RTDS/VisitOccurrence/RtdsVisitOccurrence.xml

@@ -18,7 +18,7 @@
 			and regexp_matches(NhsNumber, '\d{10}');
 	</Sql>
 	<Explanations>
-		<Explanation columnName="PatientId">
+		<Explanation columnName="NhsNumber">
 			<Description>Patient NHS Number</Description>
 			<Origin>NHS NUMBER</Origin>
 		</Explanation>

OmopTransformer/RTDS/VisitOccurrence/RtdsVisitOccurrenceRecord.cs

@@ -7,7 +7,7 @@ namespace OmopTransformer.RTDS.VisitOccurrence;
 [SourceQuery("RtdsVisitOccurrence.xml")]
 internal class RtdsVisitOccurrenceRecord
 {
-    public string? PatientId { get; set; }
+    public string? NhsNumber { get; set; }
     public string? event_start_date { get; set; }
     public string? event_end_date { get; set; }
 }

OmopTransformer/SACT/Observation/SactAdjunctiveTherapyType/SactAdjunctiveTherapyType.xml

@@ -6,8 +6,8 @@
 			Case 
 				When Adjunctive_Therapy = 1 then concat(Adjunctive_Therapy, ' - Adjuvant Therapy')
 				When Adjunctive_Therapy = 2 then concat(Adjunctive_Therapy, ' - Neoadjuvant Therapy')
-				When Intent_Of_Treatment = 3 then concat(Adjunctive_Therapy, ' - Not Applicable (Primary Treatment)')
-				When Intent_Of_Treatment = 9 then concat(Adjunctive_Therapy, ' - Not Known (Not Recorded)')
+				When Adjunctive_Therapy = 3 then concat(Adjunctive_Therapy, ' - Not Applicable (Primary Treatment)')
+				When Adjunctive_Therapy = 9 then concat(Adjunctive_Therapy, ' - Not Known (Not Recorded)')
 			else '' end as Source_value,
 		  	Administration_Date
 		from omop_staging.sact_staging

OmopTransformer/SUS/APC/Measurements/SusAPCMeasurement.cs

@@ -24,6 +24,9 @@ internal class SusAPCMeasurement : OmopMeasurement<SusAPCMeasurementRecord>
     [Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.DiagnosisICD))]
     public override int? measurement_source_concept_id { get; set; }
 
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? measurement_source_value { get; set; }
+
     [Transform(typeof(RelationshipSelector), nameof(Source.DiagnosisICD))]
     public override string? value_source_value { get; set; }
 

OmopTransformer/SUS/APC/Measurements/SusAPCMeasurementRecord.cs

@@ -3,7 +3,7 @@
 namespace OmopTransformer.SUS.APC.Measurements.SusAPCMeasurement;
 
 [DataOrigin("SUS")]
-[Description("Sus APC  Measurement")]
+[Description("Sus APC Measurement")]
 [SourceQuery("SusAPCMeasurement.xml")]
 internal class SusAPCMeasurementRecord
 {

OmopTransformer/SUS/OP/Measurements/SusOPMeasurement.cs

@@ -27,5 +27,8 @@ internal class SusOPMeasurement : OmopMeasurement<SusOPMeasurementRecord>
     [Transform(typeof(StandardMeasurementConceptSelector), useOmopTypeAsSource: true, nameof(measurement_source_concept_id))]
     public override int[]? measurement_concept_id { get; set; }
 
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? measurement_source_value { get; set; }
+
     public override bool IsValid => base.IsValid && value_source_value != null;
 }

OmopTransformer/Transformation/SactAdjunctiveTherapyTypeLookup.cs

@@ -10,8 +10,8 @@ internal class SactAdjunctiveTherapyTypeLookup : ILookup
         {
             { "1", new ValueWithNote("4191637", "Adjuvant - intent") },
             { "2", new ValueWithNote("4161587", "Neoadjuvant intent") },
-            { "3", new ValueWithNote("", "Not Applicable (Primary Treatment)") },
-            { "9" , new ValueWithNote("", "Not Known (Not Recorded)") },
+            { "3", new ValueWithNote("0", "Not Applicable (Primary Treatment)") },
+            { "9" , new ValueWithNote("0", "Not Known (Not Recorded)") },
         };
 
      public string[] ColumnNotes =>