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added endpoint J10_LOWCHRON as example #21

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Merged
javier-gracia-tabuenca-tuni merged 2 commits into from
Oct 8, 2025
Merged

added endpoint J10_LOWCHRON as example #21

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30c9450
added endpoint J10_LOWCHRON as example
javier-gracia-tabuenca-tuni Sep 29, 2025
bac802f
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javier-gracia-tabuenca-tuni Oct 8, 2025
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3 changes: 2 additions & 1 deletion R/getConceptsWithCodeCounts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
}
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4 changes: 2 additions & 2 deletions inst/testdata/config/atlasDev_databasesConfig.yml
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Expand Up @@ -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
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Binary file modified inst/testdata/data/FinnGenR13_countsOnly.sqlite
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3 changes: 2 additions & 1 deletion inst/testdata/data/createTestingData.R
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Expand Up @@ -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")
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5 changes: 4 additions & 1 deletion tests/testmanual/manualtest-timeplotview.R
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Expand Up @@ -17,10 +17,13 @@ conceptId <- 782748

conceptId <- 21602735

conceptId <- 2010001615 # test endpoint


results <- getCodeCounts(
CDMdbHandler,
conceptId = conceptId
conceptId = conceptId,
codeCountsTable = "code_counts"
)


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4 changes: 2 additions & 2 deletions tests/testthat/test-createCodeCountsTable.R
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Expand Up @@ -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 |>
Expand Down Expand Up @@ -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 |>
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