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added DRUG_STRENGTH #56

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Merged
javier-gracia-tabuenca-tuni merged 3 commits into from
Sep 30, 2025
Merged

added DRUG_STRENGTH #56

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a8e86ac
added DRUG_STRENGTH
javier-gracia-tabuenca-tuni Sep 29, 2025
deadbe7
changed DBI::dbListTables with DatabaseConnector::getTableNames
javier-gracia-tabuenca-tuni Sep 29, 2025
afbf486
Updated NEWS.md to fix warning
javier-gracia-tabuenca-tuni Sep 29, 2025
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2 changes: 1 addition & 1 deletion R/appendUsagiFileToSTCMtable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ appendUsagiFileToSTCMtable <- function(
#

# check if the sourceToConceptMapTable exists
listTables <- DBI::dbListTables(connection, vocabularyDatabaseSchema)
listTables <- DatabaseConnector::getTableNames(connection, vocabularyDatabaseSchema)
if (!sourceToConceptMapTable %in% listTables) {
stop(paste0("The sourceToConceptMapTable ", sourceToConceptMapTable, " does not exist in the vocabularyDatabaseSchema ", vocabularyDatabaseSchema))
}
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4 changes: 2 additions & 2 deletions R/databasesFromAndToCSV.R
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Expand Up @@ -24,7 +24,7 @@ omopVocabularyCSVsToDuckDB <- function(
"CONCEPT_RELATIONSHIP",
"CONCEPT_SYNONYM",
"DOMAIN",
# "DRUG_STRENGTH", TEMP: loading makes error, leave out at the moment
"DRUG_STRENGTH",
"RELATIONSHIP",
"VOCABULARY"
)
Expand Down Expand Up @@ -113,7 +113,7 @@ duckdbToOMOPVocabularyCSVs <- function(
OMOPVocabularyTableNames |>
stringr::str_to_lower() |>
checkmate::assertSubset(
DatabaseConnector::dbListTables(connection)
DatabaseConnector::getTableNames(connection)
)

pathToOMOPVocabularyCSVsFolder |> checkmate::assertDirectoryExists()
Expand Down
2 changes: 1 addition & 1 deletion R/updateUsagiFile.R
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Expand Up @@ -51,7 +51,7 @@ updateUsagiFile <- function(
# Check if required tables exist
# tables <- DatabaseConnector::getTableNames(condlnection, vocabularyDatabaseSchema)
# TEMP untill solved https://github.com/OHDSI/DatabaseConnector/issues/299
tableNames <- DatabaseConnector::dbListTables(connection, vocabularyDatabaseSchema)
tableNames <- DatabaseConnector::getTableNames(connection, vocabularyDatabaseSchema)
c("concept", "concept_relationship", "domain") |>
checkmate::assertSubset(tableNames)

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2 changes: 1 addition & 1 deletion R/validateCDMtablesWithDQD.R
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Expand Up @@ -20,7 +20,7 @@ validateCDMtablesWithDQD <- function(connectionDetails, vocabularyDatabaseSchema
validationResultsFolder |> checkmate::assertDirectory()

connection <- DatabaseConnector::connect(connectionDetails)
tableNames <- DatabaseConnector::dbListTables(connection, vocabularyDatabaseSchema)
tableNames <- DatabaseConnector::getTableNames(connection, vocabularyDatabaseSchema)
DatabaseConnector::disconnect(connection)

OMOPVocabularyTableNames <- c(
Expand Down
2 changes: 1 addition & 1 deletion R/validateUsagiFile.R
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Expand Up @@ -41,7 +41,7 @@ validateUsagiFile <- function(
# Check if required tables exist
# tables <- DatabaseConnector::getTableNames(condlnection, vocabularyDatabaseSchema)
# TEMP untill solved https://github.com/OHDSI/DatabaseConnector/issues/299
tableNames <- DatabaseConnector::dbListTables(connection, vocabularyDatabaseSchema)
tableNames <- DatabaseConnector::getTableNames(connection, vocabularyDatabaseSchema)
c("concept", "concept_relationship", "domain") |>
checkmate::assertSubset(tableNames)

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2 changes: 1 addition & 1 deletion inst/testdata/VOCABULARIES/ICD10fi/NEWS.md
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Expand Up @@ -16,4 +16,4 @@
# ICD10fi v1.0.0

- Brought from old FinOMOP "Tietoriihi" GitLab with some minor fixes.
- Mappings of 12 of the codes fixed in 2023-03.
- Mappings of 12 of the codes fixed in 2023-03.
14 changes: 7 additions & 7 deletions tests/testthat/test-appendUsagiFileToSTCMTable.R
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Expand Up @@ -28,7 +28,7 @@ test_that("test appendUsagiFileToSTCMTable appends the usagi file to the sourceT
expect_equal(nrowUsagiFile)

stcmTable |>
dplyr::filter(TARGET_CONCEPT_ID != 0L) |>
dplyr::filter(target_concept_id != 0L) |>
dplyr::count() |> dplyr::pull(n) |>
expect_equal(nrowUsagiFileMapped)

Expand Down Expand Up @@ -71,7 +71,7 @@ test_that("test appendUsagiFileToSTCMTable appends the usagi file to the sourceT
expect_equal(nrowUsagiFile)

stcmTable |>
dplyr::filter(TARGET_CONCEPT_ID != 0L) |>
dplyr::filter(target_concept_id != 0L) |>
dplyr::count() |> dplyr::pull(n) |>
expect_equal(nrowUsagiFileMapped)

Expand All @@ -84,7 +84,7 @@ test_that("test appendUsagiFileToSTCMTable appends the usagi file to the sourceT
"source_domain", "source_parents_concept_ids"))

stcmTable |>
dplyr::filter(is.na(SOURCE_PARENTS_CONCEPT_IDS)) |>
dplyr::filter(is.na(source_parents_concept_ids)) |>
nrow() |>
expect_equal(0)

Expand Down Expand Up @@ -119,14 +119,14 @@ test_that("test appendUsagiFileToSTCMTable appends the ICD10fi usagi file to the

# For source code C18.62 the parent concept IDs should be ICD10 code C18.6 with concept_id 45552246
stcmTable |>
dplyr::filter(SOURCE_CODE == "C18.62") |>
dplyr::pull(SOURCE_PARENTS_CONCEPT_IDS) |>
dplyr::filter(source_code == "C18.62") |>
dplyr::pull(source_parents_concept_ids) |>
expect_equal("45552246")

# For source code Y94.1 the parent concept IDs should be ICD10fi code Y94 with concept_id 2000503727
stcmTable |>
dplyr::filter(SOURCE_CODE == "Y94.1") |>
dplyr::pull(SOURCE_PARENTS_CONCEPT_IDS) |>
dplyr::filter(source_code == "Y94.1") |>
dplyr::pull(source_parents_concept_ids) |>
expect_equal("2000503725")

})
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