FINNGEN · javier-gracia-tabuenca-tuni · Oct 8, 2025 · Sep 22, 2025 · Sep 22, 2025 · Sep 22, 2025
diff --git a/R/getConceptsWithCodeCounts.R b/R/getConceptsWithCodeCounts.R
@@ -53,7 +53,8 @@ getConceptsWithCodeCounts <- function(
     sql <- SqlRender::translate(sql, targetDialect = connection@dbms)
     concepts <- DatabaseConnector::dbGetQuery(connection, sql) |>
         tibble::as_tibble() |>
-        dplyr::mutate(standard_concept = dplyr::if_else(is.na(standard_concept), FALSE, TRUE))
+        dplyr::mutate(standard_concept = dplyr::if_else(is.na(standard_concept), FALSE, TRUE)) |> 
+        dplyr::mutate(concept_id = as.double(concept_id))
 
     return(concepts)
 }

diff --git a/inst/sql/sql_server/createCodeCountsTable.sql b/inst/sql/sql_server/createCodeCountsTable.sql
@@ -44,6 +44,8 @@ temp_concept_ancestor AS (
         SELECT DISTINCT
             maps_to_concept_id, calendar_year, gender_concept_id, age_decile, record_counts
         FROM @resultsDatabaseSchema.@stratifiedCodeCountsTable
+        -- do not take if maps_to_concept_id is a standard concept
+        WHERE concept_id != maps_to_concept_id
      )
      GROUP BY
          maps_to_concept_id

diff --git a/inst/testdata/config/atlasDev_databasesConfig.yml b/inst/testdata/config/atlasDev_databasesConfig.yml
@@ -13,8 +13,8 @@ BQ5k:
           bigint: integer64
       tempEmulationSchema: atlas-development-270609.sandbox
     cdm:
-        cdmDatabaseSchema: atlas-development-270609.etl_sam_r12_5k_omop
-        vocabularyDatabaseSchema: atlas-development-270609.etl_sam_r12_5k_omop
+        cdmDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3_test
+        vocabularyDatabaseSchema: atlas-development-270609.finngen_omop_r13_v3_test
         resultsDatabaseSchema: atlas-development-270609.sandbox
     cohortTable:
         cohortDatabaseSchema: atlas-development-270609.sandbox

diff --git a/inst/testdata/data/FinnGenR13_countsOnly.sqlite b/inst/testdata/data/FinnGenR13_countsOnly.sqlite
diff --git a/inst/testdata/data/createTestingData.R b/inst/testdata/data/createTestingData.R
@@ -7,7 +7,8 @@ source("tests/testthat/setup.R")
 conceptIds <- c(
     317009, # Snomed: Asthma
     45596282, # ICD10: Asthma
-    21601855 # ATC level 4: C10AA (Statins)
+    21601855, # ATC level 4: C10AA (Statins)
+    2010001615 # test endpoint
 )
 
 CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")

diff --git a/tests/testmanual/manualtest-timeplotview.R b/tests/testmanual/manualtest-timeplotview.R
@@ -17,10 +17,13 @@ conceptId <- 782748
 
 conceptId <- 21602735
 
+conceptId <- 2010001615 # test endpoint
+
 
 results <- getCodeCounts(
     CDMdbHandler,
-    conceptId = conceptId
+    conceptId = conceptId, 
+    codeCountsTable = "code_counts"
 )
 
 

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -90,7 +90,7 @@ if (testingDatabase %in% c("AtlasDevelopment-DBI")) {
     pathToYalmFile = system.file("testdata", "config", "atlasDev_databasesConfig.yml", package = "ROMOPAPI")
   )
 
-  test_cohortTableHandlerConfig <- test_databasesConfig[[1]]$cohortTableHandler
+  test_cohortTableHandlerConfig <- test_databasesConfig[[2]]$cohortTableHandler
 }
 
 

diff --git a/tests/testthat/test-createCodeCountsTable.R b/tests/testthat/test-createCodeCountsTable.R
@@ -25,7 +25,7 @@ test_that("createStratifiedCodeCountsTable works with duplicated counts", {
     createStratifiedCodeCountsTable(CDMdbHandler, domains = domain, stratifiedCodeCountsTable = stratifiedCodeCountsTable)
   )
 
-  stratifiedCodeCounts <- CDMdbHandler$connectionHandler$tbl(paste0(resultsDatabaseSchema, ".", stratifiedCodeCountsTable))
+  stratifiedCodeCounts <- CDMdbHandler$connectionHandler$tbl(I(paste0(resultsDatabaseSchema, ".", stratifiedCodeCountsTable)))
 
   # check that the table was created 
   stratifiedCodeCounts |>
@@ -99,7 +99,7 @@ test_that("createCodeCountsTables works", {
   # - Check if the table was created
   resultsDatabaseSchema <- CDMdbHandler$resultsDatabaseSchema
   cdmDatabaseSchema <- CDMdbHandler$cdmDatabaseSchema
-  code_counts <- CDMdbHandler$connectionHandler$tbl(paste0(resultsDatabaseSchema, ".", codeCountsTable))
+  code_counts <- CDMdbHandler$connectionHandler$tbl(I(paste0(resultsDatabaseSchema, ".", codeCountsTable)))
 
   # check that the table was created with correct columns
   code_counts |>

diff --git a/tests/testthat/test-getConceptsWithCodeCounts.R b/tests/testthat/test-getConceptsWithCodeCounts.R
@@ -51,7 +51,7 @@ test_that("getConceptsWithCodeCounts works", {
 
   # Check that all concept_ids are unique
   result |>
-    dplyr::count(concept_id) |>
+    dplyr::count(concept_id, sort = TRUE) |>
     dplyr::filter(n > 1) |>
     nrow() |>
     expect_equal(0)
-Original file line number
+Diff line change
@@ Expand Up / @@ -90,7 +90,7 @@ if (testingDatabase %in% c("AtlasDevelopment-DBI")) { @@
         pathToYalmFile = system.file("testdata", "config", "atlasDev_databasesConfig.yml", package = "ROMOPAPI")
       )
-      test_cohortTableHandlerConfig <- test_databasesConfig[[1]]$cohortTableHandler
+      test_cohortTableHandlerConfig <- test_databasesConfig[[2]]$cohortTableHandler
     }
@@ Expand Down @@