Merge pull request #270 from answerdigital/feature/lab-observations

Feature/lab observations

Author: holtyad

OmopTransformer/LabTestLookup.cs

@@ -260,6 +260,9 @@
     <None Update="OxfordLab\Measurements\OxfordLabMeasurement.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="OxfordLab\Observations\LabReportGeneralComment\OxfordLabGeneralComment.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="OxfordSpineDeath\Death\OxfordSpineDeath.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

OmopTransformer/OmopTransformer.csproj

@@ -9,6 +9,7 @@ select
 	NORMAL_LOW,
 	NORMAL_HIGH
 from ##duckdb_source##
+where lower(EVENT) not like '%comment%'
 	</Sql>
     <Explanations>
 	    <Explanation columnName="NHS_NUMBER">

OmopTransformer/OxfordLab/Measurements/OxfordLabMeasurement.xml

@@ -0,0 +1,29 @@
+using OmopTransformer.Annotations;
+using OmopTransformer.Omop.Observation;
+using OmopTransformer.Transformation;
+
+namespace OmopTransformer.OxfordLab.Observations.LabReportGeneralComment;
+
+internal class OxfordLabGeneralComment : OmopObservation<OxfordLabGeneralCommentRecord>
+{
+    [CopyValue(nameof(Source.NHS_NUMBER))]
+    public override string? nhs_number { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.EVENT_START_DT_TM))]
+    public override DateTime? observation_date { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.EVENT_START_DT_TM))]
+    public override DateTime? observation_datetime { get; set; }
+
+    [ConstantValue(37053687, "Lab report general comments")]
+    public override int[]? observation_concept_id { get; set; }
+
+    [ConstantValue(32828, "EHR episode record")]
+    public override int? observation_type_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.@EVENT))]
+    public override string? observation_source_value { get; set; }
+
+    [CopyValue(nameof(Source.RESULT_VALUE))]
+    public override string? value_as_string { get; set; }
+}

OmopTransformer/OxfordLab/Observations/LabReportGeneralComment/OxfordLabGeneralComment.cs

@@ -0,0 +1,29 @@
+<Query>
+    <Sql type="duckdb">
+select
+    NHS_NUMBER,
+    EVENT,
+    EVENT_START_DT_TM,
+    RESULT_VALUE
+from ##duckdb_source##
+where lower(EVENT) like '%comment%'
+    </Sql>
+    <Explanations>
+        <Explanation columnName="NHS_NUMBER">
+            <Description>Patient NHS Number</Description>
+            <Origin>NHS NUMBER</Origin>
+        </Explanation>
+        <Explanation columnName="EVENT">
+            <Description>Lab test event</Description>
+            <Origin>EVENT</Origin>
+        </Explanation>
+        <Explanation columnName="EVENT_START_DT_TM">
+            <Description>Lab test event start datetime</Description>
+            <Origin>EVENT START DT TM</Origin>
+        </Explanation>
+        <Explanation columnName="RESULT_VALUE">
+            <Description>Lab report comment text</Description>
+            <Origin>RESULT VALUE</Origin>
+        </Explanation>
+    </Explanations>
+</Query>

OmopTransformer/OxfordLab/Observations/LabReportGeneralComment/OxfordLabGeneralComment.xml

@@ -0,0 +1,14 @@
+using OmopTransformer.Annotations;
+
+namespace OmopTransformer.OxfordLab.Observations.LabReportGeneralComment;
+
+[DataOrigin("OxfordLab")]
+[Description("Oxford Lab General Comment Observation")]
+[SourceQuery("OxfordLabGeneralComment.xml")]
+internal class OxfordLabGeneralCommentRecord
+{
+    public string? NHS_NUMBER { get; set; }
+    public string? @EVENT { get; set; }
+    public string? EVENT_START_DT_TM { get; set; }
+    public string? RESULT_VALUE { get; set; }
+}

OmopTransformer/OxfordLab/Observations/LabReportGeneralComment/OxfordLabGeneralCommentRecord.cs

@@ -1,21 +1,25 @@
 using Microsoft.Extensions.Logging;
 using OmopTransformer.Omop;
+using OmopTransformer.Omop.Measurement;
+using OmopTransformer.Omop.Observation;
 using OmopTransformer.OxfordLab.Measurements.OxfordLabMeasurement;
+using OmopTransformer.OxfordLab.Observations.LabReportGeneralComment;
 using OmopTransformer.Transformation;
-using OmopTransformer.Omop.Measurement;
 
 namespace OmopTransformer.OxfordLab;
 
 internal class OxfordLabTransformer : Transformer
 {
     private readonly ConceptResolver _conceptResolver;
     private readonly IMeasurementRecorder _measurementRecorder;
+    private readonly IObservationRecorder _observationRecorder;
 
     public OxfordLabTransformer(
         IRecordTransformer recordTransformer,
         TransformOptions transformOptions,
         IRecordProvider recordProvider,
         IMeasurementRecorder measurementRecorder,
+        IObservationRecorder observationRecorder,
         ConceptResolver conceptResolver,
         IRunAnalysisRecorder runAnalysisRecorder,
         ILoggerFactory loggerFactory) : base(recordTransformer,
@@ -26,6 +30,7 @@ public OxfordLabTransformer(
         loggerFactory)
     {
         _measurementRecorder = measurementRecorder;
+        _observationRecorder = observationRecorder;
         _conceptResolver = conceptResolver;
     }
 
@@ -39,6 +44,12 @@ await Transform<OxfordLabMeasurementRecord, OxfordLabMeasurement>(
             runId,
             cancellationToken);
 
+        await Transform<OxfordLabGeneralCommentRecord, OxfordLabGeneralComment>(
+            _observationRecorder.InsertUpdateObservations,
+            "Oxford Lab General Comments",
+            runId,
+            cancellationToken);
+
         _conceptResolver.PrintErrors();
     }
 }

OmopTransformer/OxfordLab/OxfordLabTransformer.cs

@@ -167,6 +167,7 @@ select
 	NORMAL_LOW,
 	NORMAL_HIGH
 from ##duckdb_source##
+where lower(EVENT) not like '%comment%'
 
 ```
 

docs/transformation-documentation/Measurement_measurement_date.md

@@ -171,6 +171,7 @@ select
 	NORMAL_LOW,
 	NORMAL_HIGH
 from ##duckdb_source##
+where lower(EVENT) not like '%comment%'
 
 ```