added 320136 # Disorder of respiratory …# big

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

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)
+    320136 # Disorder of respiratory …# big 
 )
 
 CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
@@ -17,7 +18,6 @@ helper_createSqliteDatabaseFromDatabase(
     pathToSqliteDatabase = "inst/testdata/data/FinnGenR13_countsOnly.sqlite"
 )
 
-
 # Test
 connection  <- DatabaseConnector::connect(DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = "inst/testdata/data/FinnGenR13_countsOnly.sqlite"))
 
@@ -30,6 +30,13 @@ dplyr::tbl(connection, "concept") |>
     dplyr::pull(n) |>
     expect_gt(0)
 
+dplyr::tbl(connection, "concept") |>
+    dplyr::count(concept_id) |>
+    dplyr::filter(n > 1) |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_equal(0)
+
 dplyr::tbl(connection, "concept_ancestor") |>
     dplyr::count() |>
     dplyr::pull(n) |>
@@ -40,7 +47,27 @@ dplyr::tbl(connection, "code_counts") |>
     dplyr::pull(n) |>
     expect_gt(0)
 
+dplyr::tbl(connection, "code_counts") |>
+    dplyr::count(concept_id) |>
+    dplyr::filter(n > 1) |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_equal(0)
+
+
 dplyr::tbl(connection, "stratified_code_counts") |>
     dplyr::count() |>
     dplyr::pull(n) |>
     expect_gt(0)
+
+
+# 
+Sys.setenv(HADESEXTAS_TESTING_ENVIRONMENT = "OnlyCounts-FinnGen")
+source("tests/testthat/setup.R")
+
+CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
+
+conceptId <- 317009
+
+report.html <- createReport(conceptId, CDMdbHandler, showsMappings = FALSE)
+browseURL(report.html)

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
 }
 
 

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)