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james-cockaynejames-cockayne
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Merge pull request #289 from answerdigital/feature/cosd-lung-mappings
Add COSD lung mappings
2 parents 43f32c8 + 1f09b19 commit feb25e0

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‎OmopTransformer/COSD/CosdTransformer.cs‎

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@@ -6,6 +6,16 @@
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using OmopTransformer.COSD.Colorectal.ConditionOccurrence.CosdConditionOccurrenceSecondaryDiagnosis;
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using OmopTransformer.COSD.Colorectal.ConditionOccurrence.CosdV8ConditionOccurrencePrimaryDiagnosis;
88
using OmopTransformer.COSD.Colorectal.ConditionOccurrence.CosdV8ConditionOccurrencePrimaryDiagnosisHistologyTopography;
9+
using LungV8ConditionOccurrencePrimaryDiagnosis = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosis.CosdV8LungConditionOccurrencePrimaryDiagnosis;
10+
using LungV8ConditionOccurrencePrimaryDiagnosisRecord = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosis.CosdV8LungConditionOccurrencePrimaryDiagnosisRecord;
11+
using LungV8ConditionOccurrencePrimaryDiagnosisHistologyTopography = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography;
12+
using LungV8ConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord;
13+
using LungV8ConditionOccurrenceProgression = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrenceProgression.CosdV8LungConditionOccurrenceProgression;
14+
using LungV8ConditionOccurrenceProgressionRecord = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrenceProgression.CosdV8LungConditionOccurrenceProgressionRecord;
15+
using LungV9ConditionOccurrenceProgression = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV9LungConditionOccurrenceProgression.CosdV9LungConditionOccurrenceProgression;
16+
using LungV9ConditionOccurrenceProgressionRecord = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV9LungConditionOccurrenceProgression.CosdV9LungConditionOccurrenceProgressionRecord;
17+
using LungV9ConditionOccurrenceRecurrence = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV9LungConditionOccurrenceRecurrence.CosdV9LungConditionOccurrenceRecurrence;
18+
using LungV9ConditionOccurrenceRecurrenceRecord = OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV9LungConditionOccurrenceRecurrence.CosdV9LungConditionOccurrenceRecurrenceRecord;
919
using OmopTransformer.COSD.Core.Death.v8Death;
1020
using OmopTransformer.COSD.Core.Death.v9DeathBasisOfDiagnosisCancer;
1121
using OmopTransformer.COSD.Core.Death.v9DeathDischargeDestination;
@@ -65,6 +75,14 @@
6575
using OmopTransformer.COSD.Colorectal.ProcedureOccurrence.CosdV8ProcedureOccurrenceProcedureOpcs;
6676
using OmopTransformer.COSD.Colorectal.ProcedureOccurrence.CosdV9ProcedureOccurrencePrimaryProcedureOpcs;
6777
using OmopTransformer.COSD.Colorectal.ProcedureOccurrence.CosdV9ProcedureOccurrenceProcedureOpcs;
78+
using LungV8ProcedureOccurrencePrimaryProcedureOpcs = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV8LungProcedureOccurrencePrimaryProcedureOpcs.CosdV8LungProcedureOccurrencePrimaryProcedureOpcs;
79+
using LungV8ProcedureOccurrencePrimaryProcedureOpcsRecord = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV8LungProcedureOccurrencePrimaryProcedureOpcs.CosdV8LungProcedureOccurrencePrimaryProcedureOpcsRecord;
80+
using LungV8ProcedureOccurrenceProcedureOpcs = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV8LungProcedureOccurrenceProcedureOpcs.CosdV8LungProcedureOccurrenceProcedureOpcs;
81+
using LungV8ProcedureOccurrenceProcedureOpcsRecord = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV8LungProcedureOccurrenceProcedureOpcs.CosdV8LungProcedureOccurrenceProcedureOpcsRecord;
82+
using LungV9ProcedureOccurrencePrimaryProcedureOpcs = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV9LungProcedureOccurrencePrimaryProcedureOpcs.CosdV9LungProcedureOccurrencePrimaryProcedureOpcs;
83+
using LungV9ProcedureOccurrencePrimaryProcedureOpcsRecord = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV9LungProcedureOccurrencePrimaryProcedureOpcs.CosdV9LungProcedureOccurrencePrimaryProcedureOpcsRecord;
84+
using LungV9ProcedureOccurrenceProcedureOpcs = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV9LungProcedureOccurrenceProcedureOpcs.CosdV9LungProcedureOccurrenceProcedureOpcs;
85+
using LungV9ProcedureOccurrenceProcedureOpcsRecord = OmopTransformer.COSD.Lung.ProcedureOccurrence.CosdV9LungProcedureOccurrenceProcedureOpcs.CosdV9LungProcedureOccurrenceProcedureOpcsRecord;
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using OmopTransformer.Omop;
6987
using OmopTransformer.Omop.ConditionOccurrence;
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using OmopTransformer.Omop.Death;
@@ -206,6 +224,36 @@ await Transform<CosdV8ConditionOccurrencePrimaryDiagnosisHistologyTopographyReco
206224
runId,
207225
cancellationToken);
208226

227+
await Transform<LungV8ConditionOccurrencePrimaryDiagnosisRecord, LungV8ConditionOccurrencePrimaryDiagnosis>(
228+
_conditionOccurrenceRecorder.InsertUpdateConditionOccurrence,
229+
"Cosd V8 Lung Condition Occurrence Primary Diagnosis",
230+
runId,
231+
cancellationToken);
232+
233+
await Transform<LungV8ConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord, LungV8ConditionOccurrencePrimaryDiagnosisHistologyTopography>(
234+
_conditionOccurrenceRecorder.InsertUpdateConditionOccurrence,
235+
"Cosd V8 Lung Condition Occurrence Primary Diagnosis Histology Topography",
236+
runId,
237+
cancellationToken);
238+
239+
await Transform<LungV8ConditionOccurrenceProgressionRecord, LungV8ConditionOccurrenceProgression>(
240+
_conditionOccurrenceRecorder.InsertUpdateConditionOccurrence,
241+
"Cosd V8 Lung Condition Occurrence Progression",
242+
runId,
243+
cancellationToken);
244+
245+
await Transform<LungV9ConditionOccurrenceProgressionRecord, LungV9ConditionOccurrenceProgression>(
246+
_conditionOccurrenceRecorder.InsertUpdateConditionOccurrence,
247+
"Cosd V9 Lung Condition Occurrence Progression",
248+
runId,
249+
cancellationToken);
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251+
await Transform<LungV9ConditionOccurrenceRecurrenceRecord, LungV9ConditionOccurrenceRecurrence>(
252+
_conditionOccurrenceRecorder.InsertUpdateConditionOccurrence,
253+
"Cosd V9 Lung Condition Occurrence Recurrence",
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runId,
255+
cancellationToken);
256+
209257
await Transform<CosdV8ProcedureOccurrencePrimaryProcedureOpcsRecord, CosdV8ProcedureOccurrencePrimaryProcedureOpcs>(
210258
_procedureOccurrenceRecorder.InsertUpdateProcedureOccurrence,
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"Cosd V8 Procedure Occurrence Primary Procedure Opcs",
@@ -230,6 +278,30 @@ await Transform<CosdV9ProcedureOccurrenceProcedureOpcsRecord, CosdV9ProcedureOcc
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runId,
231279
cancellationToken);
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281+
await Transform<LungV8ProcedureOccurrencePrimaryProcedureOpcsRecord, LungV8ProcedureOccurrencePrimaryProcedureOpcs>(
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_procedureOccurrenceRecorder.InsertUpdateProcedureOccurrence,
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"Cosd V8 Lung Procedure Occurrence Primary Procedure Opcs",
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runId,
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cancellationToken);
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await Transform<LungV8ProcedureOccurrenceProcedureOpcsRecord, LungV8ProcedureOccurrenceProcedureOpcs>(
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_procedureOccurrenceRecorder.InsertUpdateProcedureOccurrence,
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"Cosd V8 Lung Procedure Occurrence Procedure Opcs",
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runId,
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cancellationToken);
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293+
await Transform<LungV9ProcedureOccurrencePrimaryProcedureOpcsRecord, LungV9ProcedureOccurrencePrimaryProcedureOpcs>(
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_procedureOccurrenceRecorder.InsertUpdateProcedureOccurrence,
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"Cosd V9 Lung Procedure Occurrence Primary Procedure Opcs",
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runId,
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cancellationToken);
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await Transform<LungV9ProcedureOccurrenceProcedureOpcsRecord, LungV9ProcedureOccurrenceProcedureOpcs>(
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_procedureOccurrenceRecorder.InsertUpdateProcedureOccurrence,
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"Cosd V9 Lung Procedure Occurrence Procedure Opcs",
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runId,
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cancellationToken);
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await Transform<CosdV9TobaccoSmokingStatusRecord, CosdV9TobaccoSmokingStatus>(
234306
_observationRecorder.InsertUpdateObservations,
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"Cosd CosdV9TobaccoSmokingStatus",

‎OmopTransformer/COSD/Lung/.gitkeep‎

Whitespace-only changes.

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosis/CosdV8LungConditionOccurrencePrimaryDiagnosis.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.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosis;
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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 CosdV8LungConditionOccurrencePrimaryDiagnosis : OmopConditionOccurrence<CosdV8LungConditionOccurrencePrimaryDiagnosisRecord>
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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(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/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosis/CosdV8LungConditionOccurrencePrimaryDiagnosis.xml‎

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<Query>
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<Sql>
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with lung as (
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select
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Record ->> '$.Lung.LungCore.LungCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,
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Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as DiagnosisDate,
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Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as NonPrimaryDiagnosisDate,
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Record ->> '$.Lung.LungCore.LungCoreDiagnosis.MorphologyICDODiagnosis.@code' as CancerHistology,
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Record ->> '$.Lung.LungCore.LungCoreDiagnosis.TopographyICDO.@code' as CancerTopography,
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Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.PrimaryDiagnosis.@code'as CancerDiagnosis
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from omop_staging.cosd_staging_81 lu
12+
where lu.Type = 'LU'
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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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CancerHistology,
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CancerTopography,
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CancerDiagnosis
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from lung
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where 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="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>CLINICAL DATE CANCER DIAGNOSIS</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="CancerDiagnosis">
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<Description>The primary diagnosis code for the cancer.</Description>
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<Origin>PRIMARY DIAGNOSIS</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosis/CosdV8LungConditionOccurrencePrimaryDiagnosisRecord.cs‎

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using OmopTransformer.Annotations;
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3+
namespace OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosis;
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5+
[DataOrigin("COSD")]
6+
[Description("COSD V8 Lung Condition Occurrence Primary Diagnosis")]
7+
[SourceQuery("CosdV8LungConditionOccurrencePrimaryDiagnosis.xml")]
8+
internal class CosdV8LungConditionOccurrencePrimaryDiagnosisRecord
9+
{
10+
public string? NhsNumber { get; set; }
11+
public string? DiagnosisDate { get; set; }
12+
public string? CancerHistology { get; set; }
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public string? CancerTopography { get; set; }
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public string? CancerDiagnosis { get; set; }
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}

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography.cs‎

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using OmopTransformer.Annotations;
2+
using OmopTransformer.Omop.ConditionOccurrence;
3+
using OmopTransformer.Transformation;
4+
5+
namespace OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography;
6+
7+
[Notes(
8+
"Assumptions",
9+
"* 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.",
10+
"* 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)",
11+
"* If the same Diagnosis occurs but we have 2 separate \"basis of diagnosis\" values, then the first one will be taken only")]
12+
internal class CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography : OmopConditionOccurrence<CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord>
13+
{
14+
[CopyValue(nameof(Source.NhsNumber))]
15+
public override string? nhs_number { get; set; }
16+
17+
[Transform(typeof(DateConverter), nameof(Source.DiagnosisDate))]
18+
public override DateTime? condition_start_date { get; set; }
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20+
[ConstantValue(32828, "`EHR episode record`")]
21+
public override int? condition_type_concept_id { get; set; }
22+
23+
[Transform(typeof(Icdo3Selector), nameof(Source.CancerHistology), nameof(Source.CancerTopography))]
24+
public override int? condition_source_concept_id { get; set; }
25+
26+
[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
27+
public override int[]? condition_concept_id { get; set; }
28+
29+
[Transform(typeof(TextDeliminator), nameof(Source.CancerHistology), nameof(Source.CancerTopography))]
30+
public override string? condition_source_value { get; set; }
31+
}

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography.xml‎

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<Query>
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<Sql>
3+
with lung as (
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select
5+
Record ->> '$.Lung.LungCore.LungCoreLinkagePatientId.NHSNumber.@extension' as NHSNumber,
6+
Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.ClinicalDateCancerDiagnosis' as DiagnosisDate,
7+
Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.DateOfNonPrimaryCancerDiagnosisClinicallyAgreed' as NonPrimaryDiagnosisDate,
8+
Record ->> '$.Lung.LungCore.LungCoreDiagnosis.MorphologyICDODiagnosis.@code' as CancerHistology,
9+
Record ->> '$.Lung.LungCore.LungCoreDiagnosis.TopographyICDO.@code' as CancerTopography,
10+
Record ->> '$.Lung.LungCore.LungCoreLinkageDiagnosticDetails.PrimaryDiagnosis.@code'as CancerDiagnosis
11+
from omop_staging.cosd_staging_81 lu
12+
where lu.Type = 'LU'
13+
)
14+
15+
select
16+
distinct
17+
NHSNumber,
18+
coalesce(DiagnosisDate, NonPrimaryDiagnosisDate) as DiagnosisDate,
19+
CancerHistology,
20+
CancerTopography,
21+
CancerDiagnosis
22+
from lung
23+
where NHSNumber is not null
24+
and CancerHistology is not null
25+
and CancerTopography is not null;
26+
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</Sql>
28+
<Explanations>
29+
<Explanation columnName="NHSNumber">
30+
<Description>Patient NHS Number</Description>
31+
<Origin>NHS NUMBER</Origin>
32+
</Explanation>
33+
<Explanation columnName="DiagnosisDate">
34+
<Description>DATE OF PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date the Primary Cancer was confirmed or the Primary Cancer diagnosis was agreed.</Description>
35+
<Origin>CLINICAL DATE CANCER DIAGNOSIS</Origin>
36+
</Explanation>
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<Explanation columnName="CancerHistology">
38+
<Description>MORPHOLOGY (ICD-O CANCER TRANSFORMATION) is the morphology code of the Cancer Transformation using the ICD-O CODE.</Description>
39+
<Origin>MORPHOLOGY (ICD-O CANCER TRANSFORMATION)</Origin>
40+
</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="CancerDiagnosis">
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<Description>The primary diagnosis code for the cancer.</Description>
47+
<Origin>PRIMARY DIAGNOSIS</Origin>
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</Explanation>
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</Explanations>
50+
</Query>

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography/CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography;
4+
5+
[DataOrigin("COSD")]
6+
[Description("COSD V8 Lung Condition Occurrence Primary Diagnosis Histology Topography")]
7+
[SourceQuery("CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopography.xml")]
8+
internal class CosdV8LungConditionOccurrencePrimaryDiagnosisHistologyTopographyRecord
9+
{
10+
public string? NhsNumber { get; set; }
11+
public string? DiagnosisDate { get; set; }
12+
public string? CancerHistology { get; set; }
13+
public string? CancerTopography { get; set; }
14+
public string? CancerDiagnosis { get; set; }
15+
}

‎OmopTransformer/COSD/Lung/ConditionOccurrence/CosdV8LungConditionOccurrenceProgression/CosdV8LungConditionOccurrenceProgression.cs‎

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1+
using OmopTransformer.Annotations;
2+
using OmopTransformer.Omop.ConditionOccurrence;
3+
using OmopTransformer.Transformation;
4+
5+
namespace OmopTransformer.COSD.Lung.ConditionOccurrence.CosdV8LungConditionOccurrenceProgression;
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 CosdV8LungConditionOccurrenceProgression : OmopConditionOccurrence<CosdV8LungConditionOccurrenceProgressionRecord>
12+
{
13+
[CopyValue(nameof(Source.NhsNumber))]
14+
public override string? nhs_number { get; set; }
15+
16+
[Transform(typeof(DateConverter), nameof(Source.NonPrimaryDiagnosisDate))]
17+
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+
22+
[Transform(typeof(Icd10StandardNonStandardSelector), nameof(Source.NonPrimaryProgressionOriginalDiagnosis))]
23+
public override int? condition_source_concept_id { get; set; }
24+
25+
[Transform(typeof(StandardConditionConceptSelector), useOmopTypeAsSource: true, nameof(condition_source_concept_id))]
26+
public override int[]? condition_concept_id { get; set; }
27+
28+
[CopyValue(nameof(Source.NonPrimaryProgressionOriginalDiagnosis))]
29+
public override string? condition_source_value { get; set; }
30+
}

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