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Merge pull request #321 from tvs-sde/cosd-breast-mappings
Cosd Measurement Mappings
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‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastFamilialCancerSyndromeIndicator/CosdV8BreastFamilialCancerSyndromeIndicator.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.Observation;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastFamilialCancerSyndromeIndicator;
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[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
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internal class CosdV8BreastFamilialCancerSyndromeIndicator : OmopObservation<CosdV8BreastFamilialCancerSyndromeIndicatorRecord>
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{
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[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
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[ConstantValue(44782478, "Hereditary cancer-predisposing syndrome")]
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public override int[]? observation_concept_id { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateOnly? observation_date { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? observation_type_concept_id { get; set; }
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[CopyValue(nameof(Source.FamilialCancerSyndromeIndicator))]
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public override string? value_as_string { get; set; }
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[ConstantValue(2000500005, "Familial Cancer (Indicator)")]
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public override int? observation_source_concept_id { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastFamilialCancerSyndromeIndicator/CosdV8BreastFamilialCancerSyndromeIndicator.xml‎

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<Query>
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<Sql>
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with BR as (
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select
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Record ->> '$.Breast.BreastCore.BreastCoreReferralAndFirstStageOfPatientPathway.DateFirstSeen' as DateFirstSeen,
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Record ->> '$.Breast.BreastCore.BreastCoreReferralAndFirstStageOfPatientPathway.DateFirstSeenCancerSpecialist' as SpecialistDateFirstSeen,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,
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Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as IntegratedStageTNMStageGroupingDate,
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Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as FinalPreTreatmentTNMStageGroupingDate,
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coalesce(
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[0].CancerTreatmentStartDate',
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment.CancerTreatmentStartDate'
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) as CancerTreatmentStartDate,
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coalesce(
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[0].BreastCoreSurgery.ProcedureDate',
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment.BreastCoreSurgery.ProcedureDate'
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) as ProcedureDate,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.FamilialCancerSyndrome.@code' as FamilialCancerSyndromeIndicator,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber
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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
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distinct
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FamilialCancerSyndromeIndicator,
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NhsNumber,
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least(
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cast (DateFirstSeen as date),
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cast (SpecialistDateFirstSeen as date),
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cast (ClinicalDateCancerDiagnosis as date),
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cast (IntegratedStageTNMStageGroupingDate as date),
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cast (FinalPreTreatmentTNMStageGroupingDate as date),
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cast (CancerTreatmentStartDate as date),
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cast (ProcedureDate as date)
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) as Date
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from BR o
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where o.FamilialCancerSyndromeIndicator is not null
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and not (
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DateFirstSeen is null and
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SpecialistDateFirstSeen is null and
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ClinicalDateCancerDiagnosis is null and
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IntegratedStageTNMStageGroupingDate is null and
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FinalPreTreatmentTNMStageGroupingDate is null and
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CancerTreatmentStartDate is null and
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ProcedureDate is null
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);
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</Sql>
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<Explanations>
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<Explanation columnName="FamilialCancerSyndromeIndicator">
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<Description>Familial Cancer Syndrome Indicator</Description>
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<Origin>FamilialCancerSyndrome</Origin>
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</Explanation>
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<Explanation columnName="NhsNumber">
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<Description>Patient NHS Number</Description>
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<Origin>NHS NUMBER</Origin>
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</Explanation>
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<Explanation columnName="Date">
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<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>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastFamilialCancerSyndromeIndicator/CosdV8BreastFamilialCancerSyndromeIndicatorRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastFamilialCancerSyndromeIndicator;
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[DataOrigin("COSD")]
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[Description("COSD V8 Breast Familial Cancer Syndrome Indicator")]
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[SourceQuery("CosdV8BreastFamilialCancerSyndromeIndicator.xml")]
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internal class CosdV8BreastFamilialCancerSyndromeIndicatorRecord
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{
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public string? FamilialCancerSyndromeIndicator { get; set; }
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public string? NhsNumber { get; set; }
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public DateOnly? Date { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.Observation;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis;
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[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
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internal class CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis : OmopObservation<CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosisRecord>
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{
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[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
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[ConstantValue(4036080, "Orientation of sexual relationship")]
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public override int[]? observation_concept_id { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateOnly? observation_date { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? observation_type_concept_id { get; set; }
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[CopyValue(nameof(Source.PersonStatedSexualOrientationCodeAtDiagnosis))]
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public override string? value_as_string { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis.xml‎

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<Query>
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<Sql>
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with BR as (
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select
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Record ->> '$.Breast.BreastCore.BreastCoreDemographics.PersonStatedSexualOrientationCodeAtDiagnosis.@code' as PersonStatedSexualOrientationCodeAtDiagnosis,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,
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coalesce(
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[0].BreastCoreSurgery.ProcedureDate',
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment.BreastCoreSurgery.ProcedureDate'
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) as ProcedureDate,
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coalesce(
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[0].CancerTreatmentStartDate',
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment.CancerTreatmentStartDate'
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) as CancerTreatmentStartDate,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber
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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
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distinct
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PersonStatedSexualOrientationCodeAtDiagnosis,
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NhsNumber,
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least(
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cast (ClinicalDateCancerDiagnosis as date),
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cast (ProcedureDate as date),
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cast (CancerTreatmentStartDate as date)
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) as Date
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from BR o
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where o.PersonStatedSexualOrientationCodeAtDiagnosis is not null
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and not (
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ClinicalDateCancerDiagnosis is null and
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ProcedureDate is null and
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CancerTreatmentStartDate is null
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);
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</Sql>
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<Explanations>
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<Explanation columnName="PersonStatedSexualOrientationCodeAtDiagnosis">
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<Description>Person Stated Sexual Orientation Code At Diagnosis</Description>
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<Origin>PersonStatedSexualOrientationCodeAtDiagnosis</Origin>
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</Explanation>
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<Explanation columnName="NhsNumber">
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<Description>Patient NHS Number</Description>
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<Origin>NHS NUMBER</Origin>
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</Explanation>
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<Explanation columnName="Date">
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<Description>Approximated date from earliest available date field (diagnosis, procedure or treatment dates)</Description>
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<Origin>Multiple date sources</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis/CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosisRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis;
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[DataOrigin("COSD")]
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[Description("COSD V8 Breast Person Stated Sexual Orientation Code At Diagnosis")]
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[SourceQuery("CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosis.xml")]
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internal class CosdV8BreastPersonStatedSexualOrientationCodeAtDiagnosisRecord
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{
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public string? PersonStatedSexualOrientationCodeAtDiagnosis { get; set; }
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public string? NhsNumber { get; set; }
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public DateOnly? Date { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastSmokingStatusCode/CosdV8BreastSmokingStatusCode.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.Observation;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastSmokingStatusCode;
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[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
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internal class CosdV8BreastSmokingStatusCode : OmopObservation<CosdV8BreastSmokingStatusCodeRecord>
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{
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[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
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[ConstantValue(43054909, "Tobacco smoking status")]
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public override int[]? observation_concept_id { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateOnly? observation_date { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? observation_type_concept_id { get; set; }
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[Transform(typeof(DoubleParser), nameof(Source.SmokingStatusCode))]
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public override double? value_as_number { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastSmokingStatusCode/CosdV8BreastSmokingStatusCode.xml‎

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<Query>
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<Sql>
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with BR as (
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select
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Record ->> '$.Breast.BreastCore.BreastCoreReferralAndFirstStageOfPatientPathway.DateFirstSeen' as DateFirstSeen,
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Record ->> '$.Breast.BreastCore.BreastCoreReferralAndFirstStageOfPatientPathway.DateFirstSeenCancerSpecialist' as SpecialistDateFirstSeen,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as ClinicalDateCancerDiagnosis,
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Record ->> '$.Breast.BreastCore.BreastCoreStaging.IntegratedStageTNMStageGroupingDate' as IntegratedStageTNMStageGroupingDate,
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Record ->> '$.Breast.BreastCore.BreastCoreStaging.FinalPreTreatmentTNMStageGroupingDate' as FinalPreTreatmentTNMStageGroupingDate,
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unnest(
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[
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[Record ->> '$.Breast.BreastCore.BreastCoreTreatment.CancerTreatmentStartDate'],
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[*].CancerTreatmentStartDate'
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],
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recursive := true
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) as CancerTreatmentStartDate,
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unnest(
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[
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[Record ->> '$.Breast.BreastCore.BreastCoreTreatment.BreastCoreSurgery.ProcedureDate'],
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Record ->> '$.Breast.BreastCore.BreastCoreTreatment[*].BreastCoreSurgery.ProcedureDate'
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],
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recursive := true
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) as ProcedureDate,
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Record ->> '$.Breast.BreastCore.BreastCoreClinicalNurseSpecialistAndRiskFactorAssessments.TobaccoSmokingStatus.@code' as SmokingStatusCode,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber
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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
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distinct
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SmokingStatusCode,
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NhsNumber,
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least(
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cast (DateFirstSeen as date),
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cast (SpecialistDateFirstSeen as date),
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cast (ClinicalDateCancerDiagnosis as date),
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cast (IntegratedStageTNMStageGroupingDate as date),
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cast (FinalPreTreatmentTNMStageGroupingDate as date),
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cast (CancerTreatmentStartDate as date),
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cast (ProcedureDate as date)
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) as Date
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from BR o
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where o.SmokingStatusCode is not null
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and not (
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DateFirstSeen is null and
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SpecialistDateFirstSeen is null and
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ClinicalDateCancerDiagnosis is null and
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IntegratedStageTNMStageGroupingDate is null and
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FinalPreTreatmentTNMStageGroupingDate is null and
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CancerTreatmentStartDate is null and
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ProcedureDate is null
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);
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</Sql>
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<Explanations>
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<Explanation columnName="SmokingStatusCode">
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<Description>Smoking Status Code</Description>
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<Origin>TobaccoSmokingStatus</Origin>
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</Explanation>
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<Explanation columnName="NhsNumber">
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<Description>Patient NHS Number</Description>
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<Origin>NHS NUMBER</Origin>
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</Explanation>
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<Explanation columnName="Date">
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<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>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastSmokingStatusCode/CosdV8BreastSmokingStatusCodeRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastSmokingStatusCode;
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[DataOrigin("COSD")]
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[Description("COSD V8 Breast Smoking Status Code")]
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[SourceQuery("CosdV8BreastSmokingStatusCode.xml")]
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internal class CosdV8BreastSmokingStatusCodeRecord
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{
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public string? SmokingStatusCode { get; set; }
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public string? NhsNumber { get; set; }
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public DateOnly? Date { get; set; }
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}

‎OmopTransformer/COSD/Breast/Observation/CosdV8BreastSourceOfReferralForOutPatientsNonPrimaryCancerPathway/CosdV8BreastSourceOfReferralForOutPatientsNonPrimaryCancerPathway.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.Observation;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.Observation.CosdV8BreastSourceOfReferralForOutPatientsNonPrimaryCancerPathway;
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[Notes("Notes", DocumentationNotes.ApproximatedDatesWarning)]
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internal class CosdV8BreastSourceOfReferralForOutPatientsNonPrimaryCancerPathway : OmopObservation<CosdV8BreastSourceOfReferralForOutPatientsNonPrimaryCancerPathwayRecord>
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{
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[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
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[ConstantValue(4258129, "Referral by")]
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public override int[]? observation_concept_id { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateOnly? observation_date { get; set; }
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[CopyValue(nameof(Source.Date))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? observation_type_concept_id { get; set; }
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[CopyValue(nameof(Source.SourceOfReferralOutPatients))]
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public override string? value_as_string { get; set; }
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}

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