Removed annotation tables from schema creation

OHDSI · Feb 15, 2024 · 98d663b · 98d663b
1 parent d867c15
commit 98d663b
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Showing 4 changed files with 7 additions and 41 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Description: CohortDiagnostics is an R utility package for the development and e
     definitions across one or more data sources, facilitating reproducible research.
 Depends:
 	DatabaseConnector (>= 5.0.0),
-	FeatureExtraction (>= 3.2.0),
+	FeatureExtraction (>= 3.4.0),
 	R (>= 4.1.0)
 Imports:
   Andromeda (>= 0.6.0),

diff --git a/NEWS.md b/NEWS.md
@@ -5,9 +5,13 @@ Changes:
 
 1. Added function to make deployment to posit connect servers easier
 
-2 Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very
+2. Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very
 large cohort definitions
 
+3. Requires use of FeatureExtraction 3.4.0 to support new API
+
+4. Removed annotation tables from result schema script
+
 CohortDiagnostics 3.2.5
 =======================
 Bug Fixes:

diff --git a/R/CohortCharacterizationDiagnostics.R b/R/CohortCharacterizationDiagnostics.R
@@ -44,7 +44,7 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           cohortDatabaseSchema = cohortDatabaseSchema,
           cdmVersion = cdmVersion,
           cohortTable = cohortTable,
-          cohortId = cohortIds,
+          cohortIds = cohortIds,
           covariateSettings = covariateSettings,
           aggregated = TRUE
         )

diff --git a/inst/sql/sql_server/CreateResultsDataModel.sql b/inst/sql/sql_server/CreateResultsDataModel.sql
@@ -1,6 +1,3 @@
-{DEFAULT @annotation = annotation}
-{DEFAULT @annotation_link = annotation_link}
-{DEFAULT @annotation_attributes = annotation_attributes}
 {DEFAULT @cohort = cohort}
 {DEFAULT @cohort_count = cohort_count}
 {DEFAULT @cohort_inclusion = cohort_inclusion}
@@ -35,9 +32,6 @@
 {DEFAULT @subset_definition = subset_definition}
 
 -- Drop old tables if exist
-DROP TABLE IF EXISTS @results_schema.@annotation;
-DROP TABLE IF EXISTS @results_schema.@annotation_link;
-DROP TABLE IF EXISTS @results_schema.@annotation_attributes;
 DROP TABLE IF EXISTS @results_schema.@cohort;
 DROP TABLE IF EXISTS @results_schema.@cohort_count;
 DROP TABLE IF EXISTS @results_schema.@cohort_inclusion;
@@ -70,38 +64,6 @@ DROP TABLE IF EXISTS @results_schema.@visit_context;
 DROP TABLE IF EXISTS @results_schema.@vocabulary;
 
 -- Create tables
---Table annotation
---HINT DISTRIBUTE ON RANDOM
-CREATE TABLE @results_schema.@annotation (
-      annotation_id BIGINT NOT NULL,
-			created_by VARCHAR NOT NULL,
-			created_on BIGINT NOT NULL,
-			modified_last_on BIGINT,
-			deleted_on BIGINT,
-			annotation VARCHAR NOT NULL,
-			PRIMARY KEY(annotation_id)
-);
-
---Table annotation_link
---HINT DISTRIBUTE ON RANDOM
-CREATE TABLE @results_schema.@annotation_link (
-      annotation_id BIGINT NOT NULL DEFAULT 0,
-			diagnostics_id VARCHAR NOT NULL,
-			cohort_id BIGINT NOT NULL,
-			database_id VARCHAR NOT NULL,
-			PRIMARY KEY(annotation_id, diagnostics_id, cohort_id, database_id)
-);
-
---Table annotation_attributes
---HINT DISTRIBUTE ON RANDOM
-CREATE TABLE @results_schema.@annotation_attributes (
-      annotation_id BIGINT NOT NULL DEFAULT 0,
-			created_by VARCHAR NOT NULL,
-			annotation_attributes VARCHAR NOT NULL,
-			created_on BIGINT NOT NULL,
-			PRIMARY KEY(annotation_id, created_by)
-);
-
 --Table cohort
 --HINT DISTRIBUTE ON RANDOM
 CREATE TABLE @results_schema.@cohort (