Merge pull request #68 from answerdigital/feature/sus-transform

Feature/sus transform

OmopTransformer/OmopTransformer.csproj

@@ -291,8 +291,52 @@
     <None Update="SACT\Sact.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="SUS\APC\Observation\AnaestheticDuringLabourDelivery\SusAPCAnaestheticDuringLabourDelivery.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\AnaestheticGivenPostLabourDelivery\SusAPCAnaestheticGivenPostLabourDelivery.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\BirthWeight\SusAPCBirthWeight.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\CarerSupportIndicator\SusAPCCarerSupportIndicator.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\GestationLengthLabourOnset\SusAPCGestationLengthLabourOnset.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\NumberOfBabies\SusAPCNumberOfBabies.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Observation\TotalPreviousPregnancies\SusAPCTotalPreviousPregnancies.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="SUS\APC\Person\SusAPCPerson.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+	<None Update="SUS\APC\Location\SusAPCLocation.xml">
+		<CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	</None>
+	<None Update="SUS\APC\Death\SusAPCDeath.xml">
+		<CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	</None>
+	  <None Update="SUS\APC\ConditionOccurrence\SusAPCConditionOccurrence.xml">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	  </None>
+	  <None Update="SUS\APC\ProcedureOccurrence\SusAPCProcedureOccurrence.xml">
+	    <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	  </None>
+	  <None Update="SUS\APC\VisitDetails\SusAPCVisitDetails.xml">
+	    <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	  </None>
+	  <None Update="SUS\APC\VisitOccurrenceWithoutSpell\SusAPCVisitOccurrenceWithoutSpell.xml">
+	    <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	  </None>
+	  <None Update="SUS\APC\VisitOccurrenceWithSpell\SusAPCVisitOccurrenceWithSpell.xml">
+	    <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+	  </None>
   </ItemGroup>
-
 	<Target Name="PostBuild" AfterTargets="PostBuildEvent">
 		<ItemGroup>
 			<DocumentationDirectory Include="$(MSBuildProjectDirectory)\..\docs\transformation-documentation" />

OmopTransformer/Program.cs

@@ -27,6 +27,7 @@
 using OmopTransformer.Omop.DrugExposure;
 using OmopTransformer.Omop.Measurement;
 using OmopTransformer.Omop.Observation;
+using OmopTransformer.SUS.APC;
 using OmopTransformer.SUS.Staging.APC;
 using OmopTransformer.SUS.Staging.APC.Clearing;
 using OmopTransformer.SUS.Staging.OP;
@@ -251,6 +252,11 @@ private static async Task Main(string[] args)
                 builder.Services.AddTransient<RtdsTransformer>();
                 builder.Services.AddHostedService<RtdsTransformHostedService>();
             }
+            else if (string.Equals(transformOptions.Type, "sus-apc", StringComparison.OrdinalIgnoreCase))
+            {
+                builder.Services.AddTransient<SusAPCTransformer>();
+                builder.Services.AddHostedService<SusAPCTransformHostedService>();
+            }
             else
             {
                 await Console.Error.WriteLineAsync($"Unknown transform type {transformOptions.Type}.");

OmopTransformer/SUS/APC/ConditionOccurrence/SusAPCConditionOccurrence.cs

@@ -0,0 +1,26 @@
+using OmopTransformer.Annotations;
+using OmopTransformer.Omop.ConditionOccurrence;
+using OmopTransformer.Transformation;
+
+namespace OmopTransformer.SUS.APC.ConditionOccurrence;
+
+internal class SusAPCConditionOccurrence : OmopConditionOccurrence<SusAPCConditionOccurrenceRecord>
+{
+    [CopyValue(nameof(Source.NHSNumber))]
+    public override string? nhs_number { get; set; }
+
+    [Transform(typeof(Icd10Selector), nameof(Source.DiagnosisICD))]
+    public override int? condition_source_concept_id { get; set; }
+
+    [Transform(typeof(SnomedSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
+    public override int[]? condition_concept_id { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.CDSActivityDate))]
+    public override DateTime? condition_start_date { get; set; }
+
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? condition_source_value { get; set; }
+
+    [ConstantValue(32020, "EHR encounter diagnosis")]
+    public override int? condition_type_concept_id { get; set; }
+}

OmopTransformer/SUS/APC/ConditionOccurrence/SusAPCConditionOccurrence.xml

@@ -0,0 +1,32 @@
+<Query>
+    <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
+	</Sql>
+    <Explanations>
+		<Explanation columnName="DiagnosisICD">
+			<Description>ICD10 diagnosis code</Description>
+			<Origin>PRIMARY DIAGNOSIS (ICD)</Origin>
+		</Explanation>
+		<Explanation columnName="GeneratedRecordIdentifier">
+			<Description>CDS specific identifier that binds multiple CDS messages together.</Description>
+			<Origin>CDS RECORD IDENTIFIER</Origin>
+		</Explanation>
+		<Explanation columnName="NHSNumber">
+			<Description>Patient NHS Number</Description>
+			<Origin>NHS NUMBER</Origin>
+		</Explanation>
+		<Explanation columnName="CDSActivityDate">
+			<Description>Event date</Description>
+			<Origin>CDS ACTIVITY DATE</Origin>
+		</Explanation>
+	</Explanations>
+</Query>

OmopTransformer/SUS/APC/ConditionOccurrence/SusAPCConditionOccurrenceRecord.cs

@@ -0,0 +1,14 @@
+using OmopTransformer.Annotations;
+
+namespace OmopTransformer.SUS.APC.ConditionOccurrence;
+
+[DataOrigin("SUS")]
+[Description("SUS Inpatient Condition Occurrence")]
+[SourceQuery("SusAPCConditionOccurrence.xml")]
+internal class SusAPCConditionOccurrenceRecord
+{
+    public string? DiagnosisICD { get; set; }
+    public string? GeneratedRecordIdentifier { get; set; }
+    public string? NHSNumber { get; set; }
+    public string? CDSActivityDate { get; set; }
+}

OmopTransformer/SUS/APC/Death/SusAPCDeath.cs

@@ -0,0 +1,24 @@
+using OmopTransformer.Annotations;
+using OmopTransformer.Omop.Death;
+using OmopTransformer.Transformation;
+
+namespace OmopTransformer.SUS.APC.Death;
+
+internal class SusAPCDeath : OmopDeath<SusAPCDeathRecord>
+{
+    [CopyValue(nameof(Source.nhs_number))]
+    public override string? NhsNumber { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.death_date))]
+    public override DateTime? death_date { get; set; }
+
+    [Transform(typeof(DateAndTimeCombiner), nameof(Source.death_date), nameof(Source.death_time))]
+    public override DateTime? death_datetime { get; set; }
+
+    [CopyValue(nameof(Source.DiagnosisICD))]
+    public override string? cause_source_value { get; set; }
+
+    [Transform(typeof(Icd10Selector), nameof(Source.DiagnosisICD))]
+    public override int? cause_concept_id { get; set; }
+
+}

OmopTransformer/SUS/APC/Death/SusAPCDeath.xml

@@ -0,0 +1,50 @@
+<Query>
+    <Sql>
+		;with primarydiagnosis as (
+		select *
+		from omop_staging.sus_ICDDiagnosis
+		where IsPrimaryDiagnosis = 1
+		)
+
+		select
+		apc.NHSNumber as nhs_number,
+		max(apc.DischargeDateFromHospitalProviderSpell) as death_date,
+		max(apc.DischargeTimeHospitalProviderSpell) as death_time,
+		max(d.DiagnosisICD) as DiagnosisICD
+		from
+		omop_staging.sus_APC apc
+		left join primarydiagnosis d
+		on apc.MessageId = d.MessageId
+		where
+		apc.NHSNumber is not null and
+		apc.DischargeDateFromHospitalProviderSpell is not null and
+		(
+		apc.DischargeMethodHospitalProviderSpell = '4'
+		or (
+		apc.DischargeDestinationHospitalProviderSpell = '79'
+		and
+		apc.DischargeMethodHospitalProviderSpell != '5'
+		)
+		)
+		group by apc.NHSNumber
+	</Sql>
+
+	<Explanations>
+		<Explanation columnName="death_date">
+			<Description>Discharge date of the patient's spell.</Description>
+			<Origin>DISCHARGE DATE (HOSPITAL PROVIDER SPELL)</Origin>
+		</Explanation>
+		<Explanation columnName="nhs_number">
+			<Description>Patient NHS Number</Description>
+			<Origin>NHS NUMBER</Origin>
+		</Explanation>
+		<Explanation columnName="death_time">
+			<Description>Discharge time of the patient's spell.</Description>
+			<Origin>DISCHARGE TIME (HOSPITAL PROVIDER SPELL)</Origin>
+		</Explanation>
+		<Explanation columnName="DiagnosisICD">
+			<Description>Primary Diagnosis</Description>
+			<Origin>PRIMARY DIAGNOSIS</Origin>
+		</Explanation>
+	</Explanations>
+</Query>

OmopTransformer/SUS/APC/Death/SusAPCDeathRecord.cs

@@ -0,0 +1,14 @@
+using OmopTransformer.Annotations;
+
+namespace OmopTransformer.SUS.APC.Death;
+
+[DataOrigin("SUS")]
+[Description("SUS Inpatient Death")]
+[SourceQuery("SusAPCDeath.xml")]
+internal class SusAPCDeathRecord
+{
+    public string? nhs_number { get; set; }
+    public string? death_date { get; set; }
+    public string? death_time { get; set; }
+    public string? DiagnosisICD { get; set; }
+}

OmopTransformer/SUS/APC/Location/SusAPCLocation.cs

@@ -0,0 +1,17 @@
+using OmopTransformer.Annotations;
+using OmopTransformer.Omop.Location;
+using OmopTransformer.Transformation;
+
+namespace OmopTransformer.SUS.APC.Location;
+
+internal class SusAPCLocation : OmopLocation<SusAPCLocationRecord>
+{
+    [CopyValue(nameof(Source.NHSNumber))]
+    public override string? nhs_number { get; set; }
+
+    [Transform(typeof(PostcodeFormatter), nameof(Source.Postcode))]
+    public override string? zip { get; set; }
+
+    [CopyValue(nameof(Source.Postcode))]
+    public override string? location_source_value { get; set; }
+}

OmopTransformer/SUS/APC/Location/SusAPCLocation.xml

@@ -0,0 +1,25 @@
+<Query>
+    <Sql>
+select
+	distinct
+		Postcode,
+		NHSNumber
+from omop_staging.sus_APC
+where LocationClassAtEpisodeStartDate = '04'
+	and
+(
+	Postcode is not null
+);
+	</Sql>
+
+	<Explanations>
+		<Explanation columnName="Postcode">
+			<Description>Patient Postcode</Description>
+			<Origin>POSTCODE</Origin>
+		</Explanation>
+		<Explanation columnName="NHSNumber">
+			<Description>Patient NHS Number</Description>
+			<Origin>NHS NUMBER</Origin>
+		</Explanation>
+	</Explanations>
+</Query>

OmopTransformer/SUS/APC/Location/SusAPCLocationRecord.cs

@@ -0,0 +1,13 @@
+using OmopTransformer.Annotations;
+
+namespace OmopTransformer.SUS.APC.Location;
+
+[DataOrigin("SUS")]
+[Description("SUS Inpatient Location")]
+[SourceQuery("SusAPCLocation.xml")]
+internal class SusAPCLocationRecord
+{
+    public string? Postcode { get; set; }
+    public string? NHSNumber { get; set; }
+
+}

OmopTransformer/SUS/APC/Observation/AnaestheticDuringLabourDelivery/SusAPCAnaestheticDuringLabourDelivery.cs

@@ -0,0 +1,40 @@
+using OmopTransformer.Annotations;
+using OmopTransformer.Omop.Observation;
+using OmopTransformer.Transformation;
+
+namespace OmopTransformer.SUS.APC.Observation.AnaestheticDuringLabourDelivery;
+
+[Notes(
+    "Notes",
+    "Observations do not require a standardized test or other activity to generate clinical fact. Typical observations are medical history, family history, lifestyle choices, healthcare utilization patterns, social circumstances etc",
+    "Valid Observation Concepts are not enforced to be from any domain.  They should still be standard concepts and typically belong to the Observation or Measurement domain.",
+    "Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be stored as a Concept (value_as_concept), a numerical value (value_as_number) or a verbatim string (value_as_string)")]
+internal class SusAPCAnaestheticDuringLabourDelivery : OmopObservation<SusAPCAnaestheticDuringLabourDeliveryRecord>
+{
+    [CopyValue(nameof(Source.NHSNumber))]
+    public override string? nhs_number { get; set; }
+
+    [CopyValue(nameof(Source.GeneratedRecordIdentifier))]
+    public override string? RecordConnectionIdentifier { get; set; }
+
+    [Transform(typeof(NumberParser), nameof(Source.HospitalProviderSpellNumber))]
+    public override int? HospitalProviderSpellNumber { get; set; }
+
+    [ConstantValue(4163264, "Type of anesthetic")]
+    public override int? observation_concept_id { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.observation_date))]
+    public override DateTime? observation_date { get; set; }
+
+    [Transform(typeof(DateConverter), nameof(Source.observation_date))]
+    public override DateTime? observation_datetime { get; set; }
+
+    [ConstantValue(38000281, "Observation recorded from EHR with text result")]
+    public override int? observation_type_concept_id { get; set; }
+
+    [CopyValue(nameof(Source.AnaestheticDuringLabourDelivery))]
+    public override string? value_as_string { get; set; }
+
+    [ConstantValue(2000500001, "ANAESTHETIC GIVEN DURING LABOUR OR DELIVERY CODE")]
+    public override int? observation_source_concept_id { get; set; }
+}

OmopTransformer/SUS/APC/Observation/AnaestheticDuringLabourDelivery/SusAPCAnaestheticDuringLabourDelivery.xml

@@ -0,0 +1,43 @@
+<Query>
+    <Sql>
+select
+    apc.NHSNumber, 
+    apc.GeneratedRecordIdentifier, 
+    coalesce(max(apc.DeliveryDate), max(apc.CDSActivityDate)) as observation_date,
+	apc.HospitalProviderSpellNumber,
+    apc.AnaestheticGivenDuringLabourDelivery
+from omop_staging.sus_APC as apc
+where apc.AnaestheticGivenDuringLabourDelivery is not null
+  and apc.NHSNumber is not null
+  and apc.CdsType in ('140', '120')
+group by 
+    apc.NHSNumber, 
+    apc.GeneratedRecordIdentifier,
+	apc.HospitalProviderSpellNumber,
+    apc.DeliveryDate, 
+    apc.AnaestheticGivenDuringLabourDelivery;
+	</Sql>
+	<Explanations>
+		<Explanation columnName="NHSNumber">
+			<Description>Patient NHS Number</Description>
+			<Origin>NHS NUMBER</Origin>
+		</Explanation>
+		<Explanation columnName="GeneratedRecordIdentifier">
+			<Description>CDS specific identifier that binds multiple CDS messages together.</Description>
+			<Origin>CDS RECORD IDENTIFIER</Origin>
+		</Explanation>
+		<Explanation columnName="HospitalProviderSpellNumber">
+			<Description>CDS specific hospital spell number that binds many episodes together.</Description>
+			<Origin>HOSPITAL PROVIDER SPELL NUMBER</Origin>
+		</Explanation>
+		<Explanation columnName="observation_date">
+			<Description>Event date</Description>
+			<Origin>CDS ACTIVITY DATE</Origin>
+			<Origin>DELIVERY DATE</Origin>
+		</Explanation>
+		<Explanation columnName="AnaestheticDuringLabourDelivery">
+			<Description>Records whether anaesthetic was given during Labour/ Delivery, and the type used.</Description>
+			<Origin>ANAESTHETIC GIVEN DURING LABOUR OR DELIVERY CODE</Origin>
+		</Explanation>
+	</Explanations>
+</Query>