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khayamAminkhayamAmin
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Merge pull request #278 from answerdigital/rtds-provider-observation
Rtds - Provider and Observation
2 parents 82945ae + bf9bf7e commit f3f2347

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‎OmopTransformer/OmopTransformer.csproj‎

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<None Update="RTDS\Location\RtdsLocation.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Provider\RtdsProvider.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\ProcedureOccurrence\RtdsProcedureOccurrence.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\VisitOccurrence\RtdsVisitOccurrence.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Observation\RtdsDecisionToPerformDate\RtdsDecisionToPerformDate.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Observation\RtdsExternalBeamEnergy\RtdsExternalBeamEnergy.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Observation\RtdsNumberOfFractions\RtdsNumberOfFractions.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Observation\RtdsReferralDate\RtdsReferralDate.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="RTDS\Observation\RtdsTreatmentAnatomicalSite\RtdsTreatmentAnatomicalSite.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>
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<None Update="SACT\Person\SactPerson.xml">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</None>

‎OmopTransformer/RTDS/Observation/RtdsDecisionToPerformDate/RtdsDecisionToPerformDate.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.RTDS.Observation;
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internal class RtdsDecisionToPerformDate : OmopObservation<RtdsDecisionToPerformDateRecord>
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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(4134859, "Decision to perform date")]
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public override int[]? observation_concept_id { get; set; }
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[Transform(typeof(DateOnlyConverter), nameof(Source.DateStamp))]
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public override DateOnly? observation_date { get; set; }
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[Transform(typeof(DateAndTimeCombiner), nameof(Source.DateStamp), nameof(Source.DateStamp))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32818, "EHR administration record")]
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public override int? observation_type_concept_id { get; set; }
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[CopyValue(nameof(Source.DateStamp))]
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public override string? value_as_string { get; set; }
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}

‎OmopTransformer/RTDS/Observation/RtdsDecisionToPerformDate/RtdsDecisionToPerformDate.xml‎

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<Query>
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<Sql>
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with results as (
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select
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distinct
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(select PatientId from omop_staging.rtds_1_demographics d where d.PatientSer = dc.PatientSer limit 1) as NhsNumber,
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dc.DiagnosisCode,
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dc.DateStamp,
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from omop_staging.RTDS_5_Diagnosis_Course dc
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where dc.DiagnosisCode like 'Decision%'
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)
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select
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NhsNumber,
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DateStamp
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from results
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where
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NhsNumber is not null
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and regexp_matches(NhsNumber, '\d{10}');
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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="DateStamp">
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<Description>Decision date of treatment</Description>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/RTDS/Observation/RtdsDecisionToPerformDate/RtdsDecisionToPerformDateRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.RTDS.Observation;
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[DataOrigin("RTDS")]
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[Description("RTDS Decision To Perform Date")]
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[SourceQuery("RtdsDecisionToPerformDate.xml")]
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internal class RtdsDecisionToPerformDateRecord
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{
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public string? NhsNumber { get; set; }
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public string? DateStamp { get; set; }
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}

‎OmopTransformer/RTDS/Observation/RtdsExternalBeamEnergy/RtdsExternalBeamEnergy.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.RTDS.Observation;
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internal class RtdsExternalBeamEnergy : OmopObservation<RtdsExternalBeamEnergyRecord>
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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(4045098, "External beam radiation therapy beam energy")]
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public override int[]? observation_concept_id { get; set; }
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[Transform(typeof(DateOnlyConverter), nameof(Source.Treatmentdatetime))]
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public override DateOnly? observation_date { get; set; }
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[Transform(typeof(DateAndTimeCombiner), nameof(Source.Treatmentdatetime), nameof(Source.Treatmentdatetime))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32818, "EHR administration record")]
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public override int? observation_type_concept_id { get; set; }
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[Transform(typeof(DoubleParser), nameof(Source.CalculatedNominalEnergy))]
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public override double? value_as_number { get; set; }
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[CopyValue(nameof(Source.NominalEnergy))]
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public override string? value_source_value { get; set; }
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}

‎OmopTransformer/RTDS/Observation/RtdsExternalBeamEnergy/RtdsExternalBeamEnergy.xml‎

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<Query>
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<Sql>
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with results as (
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select distinct
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(select PatientId from omop_staging.rtds_1_demographics d where d.PatientSer = PatientSer limit 1) as NhsNumber,
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Treatmentdatetime,
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Cast(NominalEnergy as double) / 1000 as CalculatedNominalEnergy,
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NominalEnergy as NominalEnergy
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from omop_staging.RTDS_4_Exposures
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)
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select
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NhsNumber,
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Treatmentdatetime,
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CalculatedNominalEnergy,
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NominalEnergy
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from results
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where
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NhsNumber is not null
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and regexp_matches(NhsNumber, '\d{10}');
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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="Treatmentdatetime">
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<Description>Start date of treatment</Description>
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</Explanation>
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<Explanation columnName="NominalEnergy">
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<Description>RADIOTHERAPY PRESCRIBED BEAM ENERGY is the prescribed beam energy of a Radiotherapy Exposure used in External Beam Radiotherapy</Description>
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<Origin>RADIOTHERAPY PRESCRIBED BEAM ENERGY</Origin>
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</Explanation>
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<Explanation columnName="CalculatedNominalEnergy">
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<Description>RADIOTHERAPY PRESCRIBED BEAM ENERGY is the prescribed beam energy of a Radiotherapy Exposure used in External Beam Radiotherapy</Description>
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<Origin>RADIOTHERAPY PRESCRIBED BEAM ENERGY</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/RTDS/Observation/RtdsExternalBeamEnergy/RtdsExternalBeamEnergyRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.RTDS.Observation;
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[DataOrigin("RTDS")]
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[Description("RTDS External Beam Radiation Therapy Energy")]
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[SourceQuery("RtdsExternalBeamEnergy.xml")]
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internal class RtdsExternalBeamEnergyRecord
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{
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public string? NhsNumber { get; set; }
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public string? Treatmentdatetime { get; set; }
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public string? NominalEnergy { get; set; }
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public string? CalculatedNominalEnergy { get; set; }
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}

‎OmopTransformer/RTDS/Observation/RtdsNumberOfFractions/RtdsNumberOfFractions.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.RTDS.Observation;
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internal class RtdsNumberOfFractions : OmopObservation<RtdsNumberOfFractionsRecord>
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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(4037631, "Number of fractions")]
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public override int[]? observation_concept_id { get; set; }
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[Transform(typeof(DateOnlyConverter), nameof(Source.StartDateTime))]
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public override DateOnly? observation_date { get; set; }
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[Transform(typeof(DateAndTimeCombiner), nameof(Source.StartDateTime), nameof(Source.StartDateTime))]
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public override DateTime? observation_datetime { get; set; }
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[ConstantValue(32818, "EHR administration record")]
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public override int? observation_type_concept_id { get; set; }
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[Transform(typeof(DoubleParser), nameof(Source.NoFracs))]
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public override double? value_as_number { get; set; }
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[CopyValue(nameof(Source.NoFracs))]
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public override string? value_source_value { get; set; }
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}

‎OmopTransformer/RTDS/Observation/RtdsNumberOfFractions/RtdsNumberOfFractions.xml‎

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<Query>
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<Sql>
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with results as (
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select distinct
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(select PatientId from omop_staging.rtds_1_demographics d where d.PatientSer = PatientSer limit 1) as NhsNumber,
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StartDateTime,
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NoFracs
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from omop_staging.RTDS_3_Prescription
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)
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select
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NhsNumber,
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StartDateTime,
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NoFracs
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from results
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where
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NhsNumber is not null
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and regexp_matches(NhsNumber, '\d{10}');
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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="StartDateTime">
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<Description>Start date of treatment</Description>
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</Explanation>
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<Explanation columnName="NoFracs">
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<Description>The prescribed number of Radiotherapy Fractions delivered to a PATIENT as described in the Radiotherapy Plan</Description>
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<Origin>RADIOTHERAPY PRESCRIBED FRACTIONS</Origin>
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</Explanation>
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</Explanations>
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</Query>

‎OmopTransformer/RTDS/Observation/RtdsNumberOfFractions/RtdsNumberOfFractionsRecord.cs‎

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using OmopTransformer.Annotations;
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namespace OmopTransformer.RTDS.Observation;
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[DataOrigin("RTDS")]
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[Description("RTDS Number Of Fractions")]
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[SourceQuery("RtdsNumberOfFractions.xml")]
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internal class RtdsNumberOfFractionsRecord
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{
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public string? NhsNumber { get; set; }
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public string? StartDateTime { get; set; }
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public string? NoFracs { get; set; }
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}

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