Adding valueAsConceptId to covariate reference table

OHDSI · May 28, 2024 · e68fd57 · e68fd57
1 parent acb4c44
commit e68fd57
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Showing 7 changed files with 9 additions and 4 deletions.
diff --git a/inst/java/FeatureExtraction.jar b/inst/java/FeatureExtraction.jar
diff --git a/inst/java/featureExtraction-3.5.0-SNAPSHOT.jar b/inst/java/featureExtraction-3.5.0-SNAPSHOT.jar
diff --git a/inst/java/featureExtraction-3.5.1-SNAPSHOT.jar b/inst/java/featureExtraction-3.5.1-SNAPSHOT.jar
diff --git a/inst/sql/sql_server/CreateCovAnalysisRefTables.sql b/inst/sql/sql_server/CreateCovAnalysisRefTables.sql
@@ -8,7 +8,8 @@ CREATE TABLE #cov_ref (
 	covariate_id BIGINT,
 	covariate_name VARCHAR(512),
 	analysis_id INT,
-	concept_id INT
+	concept_id INT,
+	value_as_concept_id INT
 	);
 
 CREATE TABLE #analysis_ref (

diff --git a/inst/sql/sql_server/MeasObsValueAsConcept.sql b/inst/sql/sql_server/MeasObsValueAsConcept.sql
@@ -95,7 +95,8 @@ INSERT INTO #cov_ref (
 	covariate_id,
 	covariate_name,
 	analysis_id,
-	concept_id
+	concept_id,
+	value_as_concept_id
 	)
 SELECT covariate_id,
 {@temporal} ? {
@@ -120,7 +121,8 @@ SELECT covariate_id,
 }
 }
 	@analysis_id AS analysis_id,
-	no_collisions.@domain_concept_id AS concept_id
+	no_collisions.@domain_concept_id AS concept_id,
+	no_collisions.value_as_concept_id AS concept_id
 FROM (
 	SELECT covariate_id,
 	  @domain_concept_id,

diff --git a/java/org/ohdsi/featureExtraction/FeatureExtraction.java b/java/org/ohdsi/featureExtraction/FeatureExtraction.java
@@ -644,7 +644,7 @@ public static String createSql(String settings, boolean aggregated, String cohor
 		}
 
 		jsonWriter.key("sqlQueryFeatureRef");
-		jsonWriter.value("SELECT covariate_id, covariate_name, analysis_id, concept_id  FROM #cov_ref");
+		jsonWriter.value("SELECT covariate_id, covariate_name, analysis_id, concept_id, value_as_concept_id FROM #cov_ref");
 
 		jsonWriter.key("sqlQueryAnalysisRef");
 		if (temporal) {

diff --git a/tests/testthat/test-PostcoordConcepts.R b/tests/testthat/test-PostcoordConcepts.R
@@ -58,6 +58,8 @@ test_that("Postcoordinated concepts on Eunomia", {
   covariateRef <- covariateData$covariateRef %>%
     collect()
   expect_equal(covariateRef$covariateId, c(246174076422716, 246174077980716))
+  expect_equal(covariateRef$conceptId, c(3000963, 3000963))
+  expect_equal(covariateRef$valueAsConceptId, c(4083207, 4084765))
 
   analysisRef <- covariateData$analysisRef %>%
     collect()