uwrit · ndobb · Dec 15, 2020 · Nov 7, 2020 · Nov 7, 2020 · Nov 13, 2020
diff --git a/omop/5.3/0_views.sql b/omop/5.3/0_views.sql
@@ -0,0 +1,15 @@
+/**
+ * Create Views
+ */
+CREATE OR ALTER VIEW dbo.v_death
+AS
+SELECT [person_id]
+      ,[death_date]
+      ,[death_datetime]
+      ,[visit_occurrence_id] = NULL
+      ,[death_type_concept_id]
+      ,[cause_concept_id]
+      ,[cause_source_value]
+      ,[cause_source_concept_id]
+FROM [dbo].[death]
+GO
diff --git a/omop/5.3/1_sqlsets.sql b/omop/5.3/1_sqlsets.sql
@@ -0,0 +1,35 @@
+/**
+ * Leaf OMOP 5.3 bootstrap script.
+ * Assumptions: TODO
+ * License: MIT
+ */
+
+DECLARE @user NVARCHAR(20) = 'bootstrap_omop.sql'
+DECLARE @yes BIT = 1
+DECLARE @no  BIT = 0
+
+/**
+ * Add OMOP SQL Sets to be queried in Leaf.
+ */
+INSERT INTO LeafDB.app.ConceptSqlSet (SqlSetFrom, IsEncounterBased, IsEventBased, SqlFieldDate, Created, CreatedBy, Updated, UpdatedBy)
+SELECT *
+FROM (VALUES ('dbo.person',               @no,  @no,  NULL,                              GETDATE(), @user, GETDATE(), @user),                          
+             ('dbo.visit_occurrence',     @yes, @no, '@.visit_start_datetime',           GETDATE(), @user, GETDATE(), @user),
+             ('dbo.condition_occurrence', @yes, @no, '@.condition_start_datetime',       GETDATE(), @user, GETDATE(), @user),
+             ('dbo.v_death',              @yes, @no, '@.death_datetime',                 GETDATE(), @user, GETDATE(), @user),          
+             ('dbo.device_exposure',      @yes, @no, '@.device_exposure_start_datetime', GETDATE(), @user, GETDATE(), @user),  
+             ('dbo.drug_exposure',        @yes, @no, '@.drug_exposure_start_datetime',   GETDATE(), @user, GETDATE(), @user),
+             ('dbo.measurement',          @yes, @no, '@.measurement_datetime',           GETDATE(), @user, GETDATE(), @user), 
+             ('dbo.observation',          @yes, @no, '@.observation_datetime',           GETDATE(), @user, GETDATE(), @user),      
+             ('dbo.procedure_occurrence', @yes, @no, '@.procedure_datetime',             GETDATE(), @user, GETDATE(), @user)
+     ) AS X(col1,col2,col3,col4,col5,col6,col7,col8)
+
+DECLARE @sqlset_person               INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
+DECLARE @sqlset_visit_occurrence     INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')  
+DECLARE @sqlset_condition_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.condition_occurrence')  
+DECLARE @sqlset_v_death              INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.v_death')  
+DECLARE @sqlset_device_exposure      INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.device_exposure')  
+DECLARE @sqlset_drug_exposure        INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.drug_exposure')  
+DECLARE @sqlset_measurement          INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.measurement')  
+DECLARE @sqlset_observation          INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.observation')  
+DECLARE @sqlset_procedure_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.procedure_occurrence')  
diff --git a/omop/5.3/2_demographics.sql b/omop/5.3/2_demographics.sql
@@ -0,0 +1,271 @@
+/**
+ * Demographics
+ */
+
+BEGIN
+
+    DECLARE @yes BIT = 1
+    DECLARE @no  BIT = 0
+
+    DECLARE @sqlset_person               INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
+    DECLARE @sqlset_visit_occurrence     INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')  
+    DECLARE @sqlset_condition_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.condition_occurrence')  
+    DECLARE @sqlset_v_death              INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.v_death')  
+    DECLARE @sqlset_device_exposure      INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.device_exposure')  
+    DECLARE @sqlset_drug_exposure        INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.drug_exposure')  
+    DECLARE @sqlset_measurement          INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.measurement')  
+    DECLARE @sqlset_observation          INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.observation')  
+    DECLARE @sqlset_procedure_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.procedure_occurrence')  
+
+    DECLARE @demog_root   NVARCHAR(50) = 'demographics'
+    DECLARE @demog_gender NVARCHAR(50) = 'demographics:gender'
+    DECLARE @demog_ethnic NVARCHAR(50) = 'demographics:ethnicity'
+    DECLARE @demog_race   NVARCHAR(50) = 'demographics:race'
+    DECLARE @demog_age    NVARCHAR(50) = 'demographics:age'
+    DECLARE @demog_vital  NVARCHAR(50) = 'demographics:vital'
+
+    ; WITH gender AS
+    (
+        SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
+        FROM dbo.person AS X INNER JOIN dbo.concept AS C
+             ON X.gender_concept_id = C.concept_id
+        WHERE X.gender_concept_id != 0
+        GROUP BY C.concept_name, C.concept_id
+    ), ethnicity AS
+    (
+        SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
+        FROM dbo.person AS X INNER JOIN dbo.concept AS C
+             ON X.ethnicity_concept_id = C.concept_id
+        WHERE X.ethnicity_concept_id != 0
+        GROUP BY C.concept_name, C.concept_id
+    ), race AS
+    (
+        SELECT C.concept_name, C.concept_id, cnt = COUNT(DISTINCT person_id), concept_id_string = CONVERT(NVARCHAR(50), C.concept_id)
+        FROM dbo.person AS X INNER JOIN dbo.concept AS C
+             ON X.race_concept_id = C.concept_id
+        WHERE X.race_concept_id != 0
+        GROUP BY C.concept_name, C.concept_id
+    )
+
+    /* INSERT */
+    INSERT INTO LeafDB.app.Concept (ExternalId, ExternalParentId, [IsNumeric], IsParent, IsRoot, SqlSetId, SqlSetWhere, 
+                                    SqlFieldNumeric, UiDisplayName, UiDisplayText, UiDisplayUnits, UiNumericDefaultText, UiDisplayPatientCount)
+
+    /* Root */
+    SELECT ExternalId            = @demog_root
+         , ExternalParentId      = NULL
+         , [IsNumeric]           = @no
+         , IsParent              = @yes
+         , IsRoot                = @yes
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Demographics'
+         , UiDisplayText         = 'Have demographics'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
+    UNION ALL 
+
+    /* Gender */ 
+    SELECT ExternalId            = @demog_gender
+         , ExternalParentId      = @demog_root
+         , [IsNumeric]           = @no
+         , IsParent              = @yes
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Gender'
+         , UiDisplayText         = 'Have gender data'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT SUM(cnt) FROM gender)
+    UNION ALL 
+    SELECT ExternalId            = @demog_gender + ':' + X.concept_id_string
+         , ExternalParentId      = @demog_gender
+         , [IsNumeric]           = @no
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = '/* ' + X.concept_name + ' */ @.gender_concept_id = ' + X.concept_id_string
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = X.concept_name
+         , UiDisplayText         = 'Identify as ' + X.concept_name
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = X.cnt
+    FROM gender AS X     
+    UNION ALL     
+
+    /* Ethnicity */     
+    SELECT ExternalId            = @demog_ethnic
+         , ExternalParentId      = @demog_root
+         , [IsNumeric]           = @no
+         , IsParent              = @yes
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Ethncity'
+         , UiDisplayText         = 'Have ethnicity data'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT SUM(cnt) FROM ethnicity)
+    UNION ALL     
+    SELECT ExternalId            = @demog_ethnic + ':' + X.concept_id_string
+         , ExternalParentId      = @demog_ethnic
+         , [IsNumeric]           = @no
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = '/* ' + X.concept_name + ' */ @.ethnicity_concept_id = ' + X.concept_id_string
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = X.concept_name
+         , UiDisplayText         = 'Identify as ' + X.concept_name
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = X.cnt
+    FROM ethnicity AS X     
+    UNION ALL     
+
+    /* Race */     
+    SELECT ExternalId            = @demog_race
+         , ExternalParentId      = @demog_root
+         , [IsNumeric]           = @no
+         , IsParent              = @yes
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Race'
+         , UiDisplayText         = 'Have race data'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT SUM(cnt) FROM race)
+    UNION ALL     
+    SELECT ExternalId            = @demog_race + ':' + X.concept_id_string
+         , ExternalParentId      = @demog_race
+         , [IsNumeric]           = @no
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = '/* ' + X.concept_name + ' */ @.race_concept_id = ' + X.concept_id_string
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = X.concept_name
+         , UiDisplayText         = 'Identify as ' + X.concept_name
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = X.cnt
+    FROM race AS X     
+    UNION ALL     
+
+    /* Age */     
+    SELECT ExternalId            = @demog_age
+         , ExternalParentId      = @demog_root
+         , [IsNumeric]           = @yes
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = '/* Current Age */ (DATEDIFF(DAY, @.birth_datetime, GETDATE()) / 365.25)'
+         , UiDisplayName         = 'Age'
+         , UiDisplayText         = 'Are'
+         , UiDisplayUnits        = 'years old'
+         , UiNumericDefaultText  = 'any current age'
+         , UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
+    UNION ALL 
+
+    /* Vital status */     
+    SELECT ExternalId            = @demog_vital
+         , ExternalParentId      = @demog_root
+         , [IsNumeric]           = @no
+         , IsParent              = @yes
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Vital Status'
+         , UiDisplayText         = 'Are living or deceased'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person)
+    UNION ALL 
+
+    /* Living */     
+    SELECT ExternalId            = @demog_vital + ':living'
+         , ExternalParentId      = @demog_vital
+         , [IsNumeric]           = @no
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_person
+         , SqlSetWhere           = '/* Not deceased */ NOT EXISTS (SELECT 1 FROM dbo.death AS @D WHERE @.person_id = @D.person_id)'
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Living'
+         , UiDisplayText         = 'Are living or not known to be deceased'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , 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))
+    UNION ALL 
+
+    /* Deceased */     
+    SELECT ExternalId            = @demog_vital + ':deceased'
+         , ExternalParentId      = @demog_vital
+         , [IsNumeric]           = @no
+         , IsParent              = @no
+         , IsRoot                = @no
+         , SqlSetId              = @sqlset_v_death
+         , SqlSetWhere           = NULL
+         , SqlFieldNumeric       = NULL
+         , UiDisplayName         = 'Deceased'
+         , UiDisplayText         = 'Are known to be deceased'
+         , UiDisplayUnits        = NULL
+         , UiNumericDefaultText  = NULL
+         , UiDisplayPatientCount = (SELECT COUNT(*) FROM dbo.person AS P WHERE EXISTS (SELECT 1 FROM dbo.death AS D WHERE P.person_id = D.person_id))
+
+    /**
+    * Set ParentId based on ExternalIds
+    */
+    UPDATE LeafDB.app.Concept
+    SET ParentId = P.Id
+    FROM LeafDB.app.Concept AS C
+        INNER JOIN (SELECT P.Id, P.ParentId, P.ExternalId
+                    FROM LeafDB.app.Concept AS P) AS P
+                        ON C.ExternalParentID = P.ExternalID
+    WHERE C.ParentId IS NULL
+
+    /**
+    * Set RootIds
+    */
+    ; WITH roots AS
+    (
+        SELECT RootId            = C.Id
+            , RootUiDisplayName = C.UiDisplayName
+            , C.IsRoot
+            , C.Id
+            , C.ParentId
+            , C.UiDisplayName
+        FROM LeafDB.app.Concept AS C
+        WHERE C.IsRoot = 1
+
+        UNION ALL
+
+        SELECT roots.RootId
+            , roots.RootUiDisplayName
+            , C2.IsRoot
+            , C2.Id
+            , C2.ParentId
+            , C2.UiDisplayName
+        FROM roots
+            INNER JOIN LeafDB.app.Concept AS C2
+                ON C2.ParentId = roots.Id
+    )
+
+    UPDATE LeafDB.app.Concept
+    SET RootId = roots.RootId
+    FROM LeafDB.app.Concept AS C
+        INNER JOIN roots
+            ON C.Id = roots.Id
+    WHERE C.RootId IS NULL
+
+END