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Restructured into separate scripts, added Labs
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 | ||
|
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| /** | ||
| * 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) | ||
|
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||
| 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') |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,271 @@ | ||
| /** | ||
| * Demographics | ||
| */ | ||
|
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||
| BEGIN | ||
|
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| DECLARE @yes BIT = 1 | ||
| DECLARE @no BIT = 0 | ||
|
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| 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') | ||
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| 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 | ||
| ) | ||
|
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| /* INSERT */ | ||
| INSERT INTO LeafDB.app.Concept (ExternalId, ExternalParentId, [IsNumeric], IsParent, IsRoot, SqlSetId, SqlSetWhere, | ||
| SqlFieldNumeric, UiDisplayName, UiDisplayText, UiDisplayUnits, UiNumericDefaultText, UiDisplayPatientCount) | ||
|
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| /* 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 | ||
|
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||
| /* 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 | ||
|
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||
| /* 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 | ||
|
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||
| /* 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 | ||
|
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||
| /* 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 | ||
|
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||
| /* 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)) | ||
|
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||
| /** | ||
| * 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 | ||
|
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| /** | ||
| * 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 | ||
|
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||
| UNION ALL | ||
|
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| 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 | ||
| ) | ||
|
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| 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 |
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