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Merge pull request #304 from answerdigital/feature/cosd-breast-mappings
COSD breast condition / procedure mappings
2 parents 5bc1946 + 7742208 commit 289e6ab

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‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosis/CosdV8BreastConditionOccurrencePrimaryDiagnosis.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.ConditionOccurrence;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrencePrimaryDiagnosis;
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[Notes(
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"Assumptions",
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"* Any changes in a Diagnosis that may occur in later submissions, for the same Diagnosis date, is taken to be an additional diagnosis as opposed to a change (hence removal of the original)",
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"* If the same Diagnosis occurs but we have 2 separate \"basis of diagnosis\" values, then the first one will be taken only")]
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internal class CosdV8BreastConditionOccurrencePrimaryDiagnosis : OmopConditionOccurrence<CosdV8BreastConditionOccurrencePrimaryDiagnosisRecord>
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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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[Transform(typeof(DateConverter), nameof(Source.DiagnosisDate))]
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public override DateTime? condition_start_date { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? condition_type_concept_id { get; set; }
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[Transform(typeof(DataDictionaryBasisOfDiagnosisCancerLookup), nameof(Source.BasisOfDiagnosisCancer))]
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public override int? condition_status_concept_id { get; set; }
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[CopyValue(nameof(Source.BasisOfDiagnosisCancer))]
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public override string? condition_status_source_value { get; set; }
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[Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.CancerDiagnosis))]
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public override int? condition_source_concept_id { get; set; }
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[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
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public override int[]? condition_concept_id { get; set; }
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[CopyValue(nameof(Source.CancerDiagnosis))]
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public override string? condition_source_value { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosis/CosdV8BreastConditionOccurrencePrimaryDiagnosis.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 ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as DiagnosisDate,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as NonPrimaryDiagnosisDate,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.MorphologyICDODiagnosis.@code' as CancerHistology,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.TopographyICDO.@code' as CancerTopography,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.BasisOfCancerDiagnosis.@code' as BasisOfDiagnosisCancer,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.PrimaryDiagnosis.@code' as CancerDiagnosis
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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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NhsNumber,
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coalesce (DiagnosisDate, NonPrimaryDiagnosisDate) as DiagnosisDate,
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BasisOfDiagnosisCancer,
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CancerDiagnosis
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from BR
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where NhsNumber is not null and
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(
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DiagnosisDate is not null or
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NonPrimaryDiagnosisDate is not null
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);
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</Sql>
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<Explanations>
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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="DiagnosisDate">
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<Description>DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.</Description>
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<Origin>DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)</Origin>
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<Origin>DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)</Origin>
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</Explanation>
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<Explanation columnName="BasisOfDiagnosisCancer">
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<Description>The basis of how a PATIENT DIAGNOSIS relating to cancer was identified.</Description>
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<Origin>BASIS OF DIAGNOSIS (CANCER)</Origin>
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</Explanation>
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<Explanation columnName="CancerDiagnosis">
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<Description>PRIMARY DIAGNOSIS (ICD) is the International Classification of Diseases (ICD) code used to identify the PRIMARY DIAGNOSIS.</Description>
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<Origin>PRIMARY DIAGNOSIS (ICD)</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosis/CosdV8BreastConditionOccurrencePrimaryDiagnosisRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrencePrimaryDiagnosis;
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[DataOrigin("COSD")]
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[Description("Cosd V8 Breast Condition Occurrence Primary Diagnosis")]
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[SourceQuery("CosdV8BreastConditionOccurrencePrimaryDiagnosis.xml")]
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internal class CosdV8BreastConditionOccurrencePrimaryDiagnosisRecord
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{
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public string? NhsNumber { get; set; }
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public string? DiagnosisDate { get; set; }
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public string? BasisOfDiagnosisCancer { get; set; }
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public string? CancerDiagnosis { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.ConditionOccurrence;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography;
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[Notes(
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"Assumptions",
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"* For a given Diagnosis date, all valid combinations of Histology and Topography are added (thereby giving us an ICD-O-3 condition) as well as the ICD10 Diagnosis.",
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"* Any changes in a Diagnosis that may occur in later submissions, for the same Diagnosis date, is taken to be an additional diagnosis as opposed to a change (hence removal of the original)",
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"* If the same Diagnosis occurs but we have 2 separate \"basis of diagnosis\" values, then the first one will be taken only")]
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internal class CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography : OmopConditionOccurrence<CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord>
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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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[Transform(typeof(DateConverter), nameof(Source.DiagnosisDate))]
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public override DateTime? condition_start_date { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? condition_type_concept_id { get; set; }
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[Transform(typeof(DataDictionaryBasisOfDiagnosisCancerLookup), nameof(Source.BasisOfDiagnosisCancer))]
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public override int? condition_status_concept_id { get; set; }
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[CopyValue(nameof(Source.BasisOfDiagnosisCancer))]
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public override string? condition_status_source_value { get; set; }
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[Transform(typeof(Icdo3Selector), nameof(Source.CancerHistology), nameof(Source.CancerTopography))]
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public override int? condition_source_concept_id { get; set; }
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[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
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public override int[]? condition_concept_id { get; set; }
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[Transform(typeof(TextDeliminator), nameof(Source.CancerHistology), nameof(Source.CancerTopography))]
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public override string? condition_source_value { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography.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 ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NhsNumber,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as DiagnosisDate,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as NonPrimaryDiagnosisDate,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.MorphologyICDODiagnosis.@code' as CancerHistology,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.TopographyICDO.@code' as CancerTopography,
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Record ->> '$.Breast.BreastCore.BreastCoreDiagnosis.BasisOfCancerDiagnosis.@code' as BasisOfDiagnosisCancer,
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Record ->> '$.Breast.BreastCore.BreastCoreLinkageDiagnosticDetails.PrimaryDiagnosis.@code' as CancerDiagnosis
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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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NhsNumber,
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coalesce (DiagnosisDate, NonPrimaryDiagnosisDate) as DiagnosisDate,
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BasisOfDiagnosisCancer,
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CancerHistology,
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CancerTopography
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from BR
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where NhsNumber is not null and
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(
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DiagnosisDate is not null or
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NonPrimaryDiagnosisDate is not null
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)
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and (CancerHistology is not null and CancerTopography is not null)
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</Sql>
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<Explanations>
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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="DiagnosisDate">
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<Description>DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.</Description>
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<Origin>DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)</Origin>
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<Origin>DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)</Origin>
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</Explanation>
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<Explanation columnName="CancerHistology">
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<Description>MORPHOLOGY (ICD-O CANCER TRANSFORMATION) is the morphology code of the Cancer Transformation using the ICD-O CODE.</Description>
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<Origin>MORPHOLOGY (ICD-O CANCER TRANSFORMATION)</Origin>
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</Explanation>
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<Explanation columnName="CancerTopography">
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<Description>TOPOGRAPHY (ICD-O) is the topographical site of the Tumour using the ICD-O CODE.</Description>
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<Origin>TOPOGRAPHY (ICD-O)</Origin>
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</Explanation>
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<Explanation columnName="BasisOfDiagnosisCancer">
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<Description>The basis of how a PATIENT DIAGNOSIS relating to cancer was identified.</Description>
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<Origin>BASIS OF DIAGNOSIS (CANCER)</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography;
4+
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[DataOrigin("COSD")]
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[Description("Cosd V8 Breast Condition Occurrence Primary Diagnosis Histology Topography")]
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[SourceQuery("CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopography.xml")]
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internal class CosdV8BreastConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord
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{
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public string? NhsNumber { get; set; }
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public string? DiagnosisDate { get; set; }
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public string? BasisOfDiagnosisCancer { get; set; }
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public string? CancerHistology { get; set; }
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public string? CancerTopography { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrenceProgression/CosdV8BreastConditionOccurrenceProgression.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.ConditionOccurrence;
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using OmopTransformer.Transformation;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrenceProgression;
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7+
[Notes(
8+
"Assumptions",
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"* Any changes in a Diagnosis that may occur in later submissions, for the same Diagnosis date, is taken to be an additional diagnosis as opposed to a change (hence removal of the original)",
10+
"* If the same Diagnosis occurs but we have 2 separate \"basis of diagnosis\" values, then the first one will be taken only")]
11+
internal class CosdV8BreastConditionOccurrenceProgression : OmopConditionOccurrence<CosdV8BreastConditionOccurrenceProgressionRecord>
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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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[Transform(typeof(DateConverter), nameof(Source.NonPrimaryDiagnosisDate))]
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public override DateTime? condition_start_date { get; set; }
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[ConstantValue(32828, "`EHR episode record`")]
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public override int? condition_type_concept_id { get; set; }
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[Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.NonPrimaryProgressionOriginalDiagnosis))]
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public override int? condition_source_concept_id { get; set; }
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[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
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public override int[]? condition_concept_id { get; set; }
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[CopyValue(nameof(Source.NonPrimaryProgressionOriginalDiagnosis))]
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public override string? condition_source_value { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrenceProgression/CosdV8BreastConditionOccurrenceProgression.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 ->> '$.Breast.BreastCore.BreastCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,
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Record ->> '$.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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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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</Sql>
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<Explanations>
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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="NonPrimaryDiagnosisDate">
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<Description>DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date where the Non Primary Cancer PATIENT DIAGNOSIS was confirmed or agreed.</Description>
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<Origin>DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)</Origin>
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</Explanation>
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<Explanation columnName="NonPrimaryProgressionOriginalDiagnosis">
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<Description>CANCER PROGRESSION (ICD ORIGINAL) is the International Classification of Diseases (ICD) code of the original PATIENT DIAGNOSIS of the Cancer Progression.</Description>
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<Origin>CANCER PROGRESSION (ICD ORIGINAL)</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV8BreastConditionOccurrenceProgression/CosdV8BreastConditionOccurrenceProgressionRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV8BreastConditionOccurrenceProgression;
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[DataOrigin("COSD")]
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[Description("COSD V8 Breast Condition Occurrence Progression")]
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[SourceQuery("CosdV8BreastConditionOccurrenceProgression.xml")]
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internal class CosdV8BreastConditionOccurrenceProgressionRecord
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{
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public string? NhsNumber { get; set; }
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public string? NonPrimaryDiagnosisDate { get; set; }
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public string? NonPrimaryProgressionOriginalDiagnosis { get; set; }
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}

‎OmopTransformer/COSD/Breast/ConditionOccurrence/CosdV9BreastConditionOccurrencePrimaryDiagnosis/CosdV9BreastConditionOccurrencePrimaryDiagnosis.cs‎

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using OmopTransformer.Annotations;
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using OmopTransformer.Omop.ConditionOccurrence;
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using OmopTransformer.Transformation;
4+
5+
namespace OmopTransformer.COSD.Breast.ConditionOccurrence.CosdV9BreastConditionOccurrencePrimaryDiagnosis;
6+
7+
[Notes(
8+
"Assumptions",
9+
"* Any changes in a Diagnosis that may occur in later submissions, for the same Diagnosis date, is taken to be an additional diagnosis as opposed to a change (hence removal of the original)",
10+
"* If the same Diagnosis occurs but we have 2 separate \"basis of diagnosis\" values, then the first one will be taken only")]
11+
internal class CosdV9BreastConditionOccurrencePrimaryDiagnosis : OmopConditionOccurrence<CosdV9BreastConditionOccurrencePrimaryDiagnosisRecord>
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{
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[CopyValue(nameof(Source.NhsNumber))]
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public override string? nhs_number { get; set; }
15+
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[Transform(typeof(DateConverter), nameof(Source.DateOfPrimaryDiagnosisClinicallyAgreed))]
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public override DateTime? condition_start_date { get; set; }
18+
19+
[ConstantValue(32828, "`EHR episode record`")]
20+
public override int? condition_type_concept_id { get; set; }
21+
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[Transform(typeof(DataDictionaryBasisOfDiagnosisCancerLookup), nameof(Source.BasisOfDiagnosisCancer))]
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public override int? condition_status_concept_id { get; set; }
24+
25+
[CopyValue(nameof(Source.BasisOfDiagnosisCancer))]
26+
public override string? condition_status_source_value { get; set; }
27+
28+
[Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.CancerDiagnosis))]
29+
public override int? condition_source_concept_id { get; set; }
30+
31+
[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
32+
public override int[]? condition_concept_id { get; set; }
33+
34+
[CopyValue(nameof(Source.CancerDiagnosis))]
35+
public override string? condition_source_value { get; set; }
36+
}

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