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khayamAminkhayamAmin
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Merge pull request #330 from tvs-sde/feature-sus-regression-fixes
Feature sus regression fixes
2 parents 9a9e592 + 62f2c67 commit 264591a

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‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrenceProgression/CosdV8BreastConditionOccurrenceProgression.xml‎

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@@ -2,20 +2,20 @@
22
<Sql>
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with BR as (
44
select
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Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as NonPrimaryDiagnosisDate,
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Record ->> '$.Breast.BreastCore.BreastCoreNonPrimaryCancerPathwayRoute.CancerProgressionICD.@code' as NonPrimaryProgressionOriginalDiagnosis
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from omop_staging.cosd_staging_81
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where type = 'BR'
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)
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select distinct
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NHSNumber,
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NhsNumber,
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NonPrimaryDiagnosisDate,
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NonPrimaryProgressionOriginalDiagnosis
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from BR
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where NonPrimaryProgressionOriginalDiagnosis is not null
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and NonPrimaryDiagnosisDate is not null
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and NHSNumber is not null;
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and NhsNumber is not null;
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</Sql>
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<Explanations>
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<Explanation columnName="NhsNumber">

OmopTransformer/COSD/Breast/Observation/DocumentationNotes.cs renamed to OmopTransformer/COSD/Breast/DocumentationNotes.cs

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@@ -1,4 +1,4 @@
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namespace OmopTransformer.COSD.Breast.Observation;
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namespace OmopTransformer.COSD.Breast;
22

33
internal class DocumentationNotes
44
{

‎OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementAdultComorbidityEvaluation/CosdV8BreastMeasurementAdultComorbidityEvaluation.cs‎

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1+
using OmopTransformer.Annotations;
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using OmopTransformer.COSD.Breast.Observation;
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using OmopTransformer.Omop.Measurement;
4+
using OmopTransformer.Transformation;
5+
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namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementAdultComorbidityEvaluation;
7+
8+
[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
9+
internal class CosdV8BreastMeasurementAdultComorbidityEvaluation : OmopMeasurement<CosdV8BreastMeasurementAdultComorbidityEvaluationRecord>
10+
{
11+
[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
13+
14+
[Transform(typeof(DateConverter), nameof(Source.MeasurementDate))]
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public override DateTime? measurement_date { get; set; }
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17+
[Transform(typeof(DateConverter), nameof(Source.MeasurementDate))]
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public override DateTime? measurement_datetime { get; set; }
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[ConstantValue(32828, "EHR episode record")]
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public override int? measurement_type_concept_id { get; set; }
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[CopyValue(nameof(Source.AdultComorbidityEvaluation))]
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public override string? measurement_source_value { get; set; }
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[ConstantValue(40488785, "Adult comorbidity evaluation-27")]
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public override int[]? measurement_concept_id { get; set; }
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[Transform(typeof(DoubleParser), nameof(Source.AdultComorbidityEvaluation))]
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public override double? value_as_number { get; set; }
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}

OmopTransformer/COSD/Breast/Observation/CosdV8BreastAdultComorbidityEvaluation/CosdV8BreastAdultComorbidityEvaluation.xml renamed to OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementAdultComorbidityEvaluation/CosdV8BreastMeasurementAdultComorbidityEvaluation.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@ select
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cast (FinalPreTreatmentTNMStageGroupingDate as date),
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cast (CancerTreatmentStartDate as date),
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cast (ProcedureDate as date)
29-
) as Date
29+
) as MeasurementDate
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from BR o
3131
where o.AdultComorbidityEvaluation is not null
3232
and not (
@@ -44,7 +44,7 @@ where o.AdultComorbidityEvaluation is not null
4444
<Description>Patient NHS Number</Description>
4545
<Origin>NHS NUMBER</Origin>
4646
</Explanation>
47-
<Explanation columnName="Date">
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<Explanation columnName="MeasurementDate">
4848
<Description>Approximated date from earliest available date field (first seen, diagnosis, staging, or treatment dates)</Description>
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<Origin>Multiple date sources</Origin>
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</Explanation>

‎OmopTransformer/COSD/Breast/Measurements/CosdV8BreastMeasurementAdultComorbidityEvaluation/CosdV8BreastMeasurementAdultComorbidityEvaluationRecord.cs‎

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using OmopTransformer.Annotations;
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3+
namespace OmopTransformer.COSD.Breast.Measurements.CosdV8BreastMeasurementAdultComorbidityEvaluation;
4+
5+
[DataOrigin("COSD")]
6+
[Description("CosdV8BreastMeasurementAdultComorbidityEvaluation")]
7+
[SourceQuery("CosdV8BreastMeasurementAdultComorbidityEvaluation.xml")]
8+
internal class CosdV8BreastMeasurementAdultComorbidityEvaluationRecord
9+
{
10+
public string? NhsNumber { get; set; }
11+
public string? MeasurementDate { get; set; }
12+
public string? AdultComorbidityEvaluation { get; set; }
13+
}

‎OmopTransformer/COSD/Breast/Measurements/CosdV9BreastMeasurementAdultComorbidityEvaluation/CosdV9BreastMeasurementAdultComorbidityEvaluation.cs‎

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using OmopTransformer.Annotations;
2+
using OmopTransformer.COSD.Breast.Measurements.CosdV9BreastMeasurementAdultComorbidityEvaluation;
3+
using OmopTransformer.Omop.Measurement;
4+
using OmopTransformer.Transformation;
5+
6+
namespace OmopTransformer.COSD.Breast.Measurements.CosdV9MeasurementAdultComorbidityEvaluation;
7+
8+
[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
9+
internal class CosdV9BreastMeasurementAdultComorbidityEvaluation : OmopMeasurement<CosdV9BreastMeasurementAdultComorbidityEvaluationRecord>
10+
{
11+
[CopyValue(nameof(Source.NhsNumber))]
12+
public override string? nhs_number { get; set; }
13+
14+
[Transform(typeof(DateConverter), nameof(Source.MeasurementDate))]
15+
public override DateTime? measurement_date { get; set; }
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[Transform(typeof(DateConverter), nameof(Source.MeasurementDate))]
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public override DateTime? measurement_datetime { get; set; }
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20+
[ConstantValue(32828, "EHR episode record")]
21+
public override int? measurement_type_concept_id { get; set; }
22+
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[CopyValue(nameof(Source.AdultComorbidityEvaluation))]
24+
public override string? measurement_source_value { get; set; }
25+
26+
[ConstantValue(40488785, "Adult comorbidity evaluation-27")]
27+
public override int[]? measurement_concept_id { get; set; }
28+
29+
[Transform(typeof(DoubleParser), nameof(Source.AdultComorbidityEvaluation))]
30+
public override double? value_as_number { get; set; }
31+
32+
}

OmopTransformer/COSD/Breast/Observation/CosdV9BreastAdultComorbidityEvaluation/CosdV9BreastAdultComorbidityEvaluation.xml renamed to OmopTransformer/COSD/Breast/Measurements/CosdV9BreastMeasurementAdultComorbidityEvaluation/CosdV9BreastMeasurementAdultComorbidityEvaluation.xml

Lines changed: 2 additions & 2 deletions
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@@ -33,7 +33,7 @@ select
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cast(StageDateIntegratedStage as date),
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cast(TreatmentStartDateCancer as date),
3535
cast(ProcedureDate as date)
36-
) as Date
36+
) as MeasurementDate
3737
from BR o
3838
where o.AdultComorbidityEvaluation is not null
3939
and not (
@@ -55,7 +55,7 @@ where o.AdultComorbidityEvaluation is not null
5555
<Description>Patient NHS Number</Description>
5656
<Origin>NHS NUMBER</Origin>
5757
</Explanation>
58-
<Explanation columnName="Date">
58+
<Explanation columnName="MeasurementDate">
5959
<Description>Approximated date from earliest available date field (first seen, diagnosis, staging, or treatment dates)</Description>
6060
<Origin>Multiple date sources</Origin>
6161
</Explanation>

‎OmopTransformer/COSD/Breast/Measurements/CosdV9BreastMeasurementAdultComorbidityEvaluation/CosdV9BreastMeasurementAdultComorbidityEvaluationRecord.cs‎

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using OmopTransformer.Annotations;
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3+
namespace OmopTransformer.COSD.Breast.Measurements.CosdV9BreastMeasurementAdultComorbidityEvaluation;
4+
5+
[DataOrigin("COSD")]
6+
[Description("CosdV9BreastMeasurementAdultComorbidityEvaluation")]
7+
[SourceQuery("CosdV9BreastMeasurementAdultComorbidityEvaluation.xml")]
8+
internal class CosdV9BreastMeasurementAdultComorbidityEvaluationRecord
9+
{
10+
public string? NhsNumber { get; set; }
11+
public string? MeasurementDate { get; set; }
12+
public string? AdultComorbidityEvaluation { get; set; }
13+
}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastAdultComorbidityEvaluation/CosdV8BreastAdultComorbidityEvaluation.cs‎

Lines changed: 0 additions & 28 deletions
This file was deleted.

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastAdultComorbidityEvaluation/CosdV8BreastAdultComorbidityEvaluationRecord.cs‎

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