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ndobbndobb
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Merge pull request #2 from uwrit/omop_bootstrap
Omop bootstrap
2 parents 70a8fbc + 3689dc7 commit 616b926

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‎omop/5.3/0_views.sql‎

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/**
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* Create Views
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*/
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CREATE OR ALTER VIEW dbo.v_death
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AS
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SELECT [person_id]
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,[death_date]
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,[death_datetime]
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,[visit_occurrence_id] = NULL
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,[death_type_concept_id]
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,[cause_concept_id]
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,[cause_source_value]
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,[cause_source_concept_id]
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FROM [dbo].[death]
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GO

‎omop/5.3/1_sqlsets.sql‎

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/**
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* Leaf OMOP 5.3 bootstrap script.
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* Assumptions: TODO
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* License: MIT
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*/
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DECLARE @user NVARCHAR(20) = 'bootstrap_omop.sql'
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DECLARE @yes BIT = 1
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DECLARE @no BIT = 0
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/**
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* Add OMOP SQL Sets to be queried in Leaf.
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*/
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INSERT INTO LeafDB.app.ConceptSqlSet (SqlSetFrom, IsEncounterBased, IsEventBased, SqlFieldDate, Created, CreatedBy, Updated, UpdatedBy)
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SELECT *
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FROM (VALUES ('dbo.person', @no, @no, NULL, GETDATE(), @user, GETDATE(), @user),
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('dbo.visit_occurrence', @yes, @no, '@.visit_start_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.condition_occurrence', @yes, @no, '@.condition_start_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.v_death', @yes, @no, '@.death_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.device_exposure', @yes, @no, '@.device_exposure_start_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.drug_exposure', @yes, @no, '@.drug_exposure_start_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.measurement', @yes, @no, '@.measurement_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.observation', @yes, @no, '@.observation_datetime', GETDATE(), @user, GETDATE(), @user),
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('dbo.procedure_occurrence', @yes, @no, '@.procedure_datetime', GETDATE(), @user, GETDATE(), @user)
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) AS X(col1,col2,col3,col4,col5,col6,col7,col8)
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DECLARE @sqlset_person INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
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DECLARE @sqlset_visit_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')
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DECLARE @sqlset_condition_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.condition_occurrence')
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DECLARE @sqlset_v_death INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.v_death')
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DECLARE @sqlset_device_exposure INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.device_exposure')
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DECLARE @sqlset_drug_exposure INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.drug_exposure')
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DECLARE @sqlset_measurement INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.measurement')
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DECLARE @sqlset_observation INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.observation')
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DECLARE @sqlset_procedure_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.procedure_occurrence')

‎omop/5.3/2_demographics.sql‎

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/**
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* Demographics
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*/
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BEGIN
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DECLARE @yes BIT = 1
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DECLARE @no BIT = 0
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DECLARE @sqlset_person INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
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DECLARE @sqlset_visit_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')
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DECLARE @sqlset_condition_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.condition_occurrence')
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DECLARE @sqlset_v_death INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.v_death')
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DECLARE @sqlset_device_exposure INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.device_exposure')
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DECLARE @sqlset_drug_exposure INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.drug_exposure')
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DECLARE @sqlset_measurement INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.measurement')
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DECLARE @sqlset_observation INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.observation')
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DECLARE @sqlset_procedure_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.procedure_occurrence')
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DECLARE @demog_root NVARCHAR(50) = 'demographics'
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DECLARE @demog_gender NVARCHAR(50) = 'demographics:gender'
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DECLARE @demog_ethnic NVARCHAR(50) = 'demographics:ethnicity'
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DECLARE @demog_race NVARCHAR(50) = 'demographics:race'
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DECLARE @demog_age NVARCHAR(50) = 'demographics:age'
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DECLARE @demog_vital NVARCHAR(50) = 'demographics:vital'
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; WITH gender AS
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(
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SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
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FROM dbo.person AS X INNER JOIN dbo.concept AS C
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ON X.gender_concept_id = C.concept_id
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WHERE X.gender_concept_id != 0
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GROUP BY C.concept_name, C.concept_id
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), ethnicity AS
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(
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SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
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FROM dbo.person AS X INNER JOIN dbo.concept AS C
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ON X.ethnicity_concept_id = C.concept_id
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WHERE X.ethnicity_concept_id != 0
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GROUP BY C.concept_name, C.concept_id
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), race AS
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(
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SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
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FROM dbo.person AS X INNER JOIN dbo.concept AS C
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ON X.race_concept_id = C.concept_id
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WHERE X.race_concept_id != 0
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GROUP BY C.concept_name, C.concept_id
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)
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/* INSERT */
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INSERT INTO LeafDB.app.Concept (ExternalId, ExternalParentId, [IsNumeric], IsParent, IsRoot, SqlSetId, SqlSetWhere,
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SqlFieldNumeric, UiDisplayName, UiDisplayText, UiDisplayUnits, UiNumericDefaultText, UiDisplayPatientCount)
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/* Root */
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SELECT ExternalId = @demog_root
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, ExternalParentId = NULL
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @yes
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Demographics'
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, UiDisplayText = 'Have demographics'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
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UNION ALL
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/* Gender */
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SELECT ExternalId = @demog_gender
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, ExternalParentId = @demog_root
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Gender'
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, UiDisplayText = 'Have gender data'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT SUM(cnt) FROM gender)
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UNION ALL
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SELECT ExternalId = @demog_gender + ':' + X.concept_id_string
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, ExternalParentId = @demog_gender
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '/* ' + X.concept_name + ' */ @.gender_concept_id = ' + X.concept_id_string
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, SqlFieldNumeric = NULL
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, UiDisplayName = X.concept_name
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, UiDisplayText = 'Identify as ' + X.concept_name
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = X.cnt
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FROM gender AS X
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UNION ALL
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/* Ethnicity */
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SELECT ExternalId = @demog_ethnic
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, ExternalParentId = @demog_root
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Ethncity'
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, UiDisplayText = 'Have ethnicity data'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT SUM(cnt) FROM ethnicity)
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UNION ALL
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SELECT ExternalId = @demog_ethnic + ':' + X.concept_id_string
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, ExternalParentId = @demog_ethnic
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '/* ' + X.concept_name + ' */ @.ethnicity_concept_id = ' + X.concept_id_string
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, SqlFieldNumeric = NULL
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, UiDisplayName = X.concept_name
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, UiDisplayText = 'Identify as ' + X.concept_name
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = X.cnt
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FROM ethnicity AS X
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UNION ALL
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/* Race */
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SELECT ExternalId = @demog_race
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, ExternalParentId = @demog_root
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Race'
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, UiDisplayText = 'Have race data'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT SUM(cnt) FROM race)
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UNION ALL
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SELECT ExternalId = @demog_race + ':' + X.concept_id_string
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, ExternalParentId = @demog_race
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '/* ' + X.concept_name + ' */ @.race_concept_id = ' + X.concept_id_string
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, SqlFieldNumeric = NULL
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, UiDisplayName = X.concept_name
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, UiDisplayText = 'Identify as ' + X.concept_name
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = X.cnt
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FROM race AS X
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UNION ALL
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/* Age */
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SELECT ExternalId = @demog_age
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, ExternalParentId = @demog_root
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, [IsNumeric] = @yes
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = '/* Current Age */ (DATEDIFF(DAY, @.birth_datetime, GETDATE()) / 365.25)'
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, UiDisplayName = 'Age'
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, UiDisplayText = 'Are'
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, UiDisplayUnits = 'years old'
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, UiNumericDefaultText = 'any current age'
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
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UNION ALL
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/* Vital status */
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SELECT ExternalId = @demog_vital
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, ExternalParentId = @demog_root
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Vital Status'
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, UiDisplayText = 'Are living or deceased'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
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UNION ALL
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/* Living */
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SELECT ExternalId = @demog_vital + ':living'
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, ExternalParentId = @demog_vital
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '/* Not deceased */ NOT EXISTS (SELECT 1 FROM dbo.death AS @D WHERE @.person_id = @D.person_id)'
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Living'
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, UiDisplayText = 'Are living or not known to be deceased'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person AS P WHERE NOT EXISTS (SELECT 1 FROM dbo.death AS D WHERE P.person_id = D.person_id))
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UNION ALL
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/* Deceased */
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SELECT ExternalId = @demog_vital + ':deceased'
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, ExternalParentId = @demog_vital
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_v_death
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Deceased'
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, UiDisplayText = 'Are known to be deceased'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person AS P WHERE EXISTS (SELECT 1 FROM dbo.death AS D WHERE P.person_id = D.person_id))
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/**
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* Set ParentId based on ExternalIds
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*/
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UPDATE LeafDB.app.Concept
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SET ParentId = P.Id
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FROM LeafDB.app.Concept AS C
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INNER JOIN (SELECT P.Id, P.ParentId, P.ExternalId
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FROM LeafDB.app.Concept AS P) AS P
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ON C.ExternalParentID = P.ExternalID
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WHERE C.ParentId IS NULL
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/**
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* Set RootIds
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*/
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; WITH roots AS
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(
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SELECT RootId = C.Id
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, RootUiDisplayName = C.UiDisplayName
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, C.IsRoot
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, C.Id
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, C.ParentId
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, C.UiDisplayName
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FROM LeafDB.app.Concept AS C
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WHERE C.IsRoot = 1
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UNION ALL
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SELECT roots.RootId
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, roots.RootUiDisplayName
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, C2.IsRoot
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, C2.Id
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, C2.ParentId
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, C2.UiDisplayName
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FROM roots
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INNER JOIN LeafDB.app.Concept AS C2
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ON C2.ParentId = roots.Id
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)
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UPDATE LeafDB.app.Concept
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SET RootId = roots.RootId
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FROM LeafDB.app.Concept AS C
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INNER JOIN roots
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ON C.Id = roots.Id
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WHERE C.RootId IS NULL
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END

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