Merge pull request #58 from FinOMOP/development

javier-gracia-tabuenca-tuni · web-flow · commit 1cca459bcef5 · 2025-09-30T11:43:33.000+03:00
v2.1.0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ROMOPMappingTools
 Title: Tools for Working with OMOP CDM Mappings
-Version: 2.0.4
+Version: 2.1.0
 Authors@R: 
     person("Javier", "Gracia-Tabuenca", , "javier.graciatabuenca@tuni.fi", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2455-0598"))
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# ROMOPMappingTools 2.1.0
+
+- Fixed concept_ancestor table generation. ICD10fi hierarchy was not correct, and duplicated rows were present in the table.
+- Added DRUG_STRENGTH table generation. This was missing, and created warnings in the DQD validation.
+- Fixed errors due to DatabaseConnector v7.0.0.
+
 # ROMOPMappingTools 2.0.5
 
 - Fixed a bug in Usagi to STCM table conversion with respect to source parents
diff --git a/R/appendUsagiFileToSTCMtable.R b/R/appendUsagiFileToSTCMtable.R
@@ -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))
     }
diff --git a/R/databasesFromAndToCSV.R b/R/databasesFromAndToCSV.R
@@ -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"
     )
@@ -113,7 +113,7 @@ duckdbToOMOPVocabularyCSVs <- function(
     OMOPVocabularyTableNames |>
         stringr::str_to_lower() |>
         checkmate::assertSubset(
-            DatabaseConnector::dbListTables(connection)
+            DatabaseConnector::getTableNames(connection)
         )
 
     pathToOMOPVocabularyCSVsFolder |> checkmate::assertDirectoryExists()
diff --git a/R/updateUsagiFile.R b/R/updateUsagiFile.R
@@ -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)
 
diff --git a/R/validateCDMtablesWithDQD.R b/R/validateCDMtablesWithDQD.R
@@ -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(
diff --git a/R/validateUsagiFile.R b/R/validateUsagiFile.R
@@ -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)
 
diff --git a/inst/sql/sql_server/CONCEPT_RELATIONSHIPToANCESTOR.sql b/inst/sql/sql_server/CONCEPT_RELATIONSHIPToANCESTOR.sql
@@ -76,8 +76,13 @@ WITH RECURSIVE ancestor_cte AS (
     FROM #relationships
   ) AS r
 )
-SELECT DISTINCT *
-FROM ancestor_cte_self_reference;
+SELECT 
+    ancestor_concept_id,
+    descendant_concept_id,
+    MIN(min_levels_of_separation) as min_levels_of_separation,
+    MAX(max_levels_of_separation) as max_levels_of_separation
+FROM ancestor_cte_self_reference
+GROUP BY ancestor_concept_id, descendant_concept_id;
 
 
 -- 4- Remove the temporary table
diff --git a/inst/testdata/VOCABULARIES/ICD10fi/NEWS.md b/inst/testdata/VOCABULARIES/ICD10fi/NEWS.md
@@ -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.
diff --git a/tests/testthat/test-appendUsagiFileToSTCMTable.R b/tests/testthat/test-appendUsagiFileToSTCMTable.R
@@ -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)
 
@@ -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)
 
@@ -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)
 
@@ -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")
 
 })
diff --git a/tests/testthat/test-conceptRelationshipToAncestorTables.R b/tests/testthat/test-conceptRelationshipToAncestorTables.R
@@ -42,4 +42,12 @@ test_that("conceptRelationshipToAncestorTables creates CONCEPT_ANCESTOR table fr
     dplyr::pull(n) |>
     expect_equal(c(1,8,16))
 
+
+    # check ancestor_concept_id and descendant_concept_id are unique
+    ancestor |>
+        dplyr::distinct(ancestor_concept_id, descendant_concept_id) |>
+        nrow() |>
+        expect_equal(ancestor |> nrow())
+
+
 })

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,7 @@ appendUsagiFileToSTCMtable <- function(`
`67`	`67`	`#`
`68`	`68`
`69`	`69`	`# check if the sourceToConceptMapTable exists`
`70`		`- listTables <- DBI::dbListTables(connection, vocabularyDatabaseSchema)`
	`70`	`+ listTables <- DatabaseConnector::getTableNames(connection, vocabularyDatabaseSchema)`
`71`	`71`	`if (!sourceToConceptMapTable %in% listTables) {`
`72`	`72`	`stop(paste0("The sourceToConceptMapTable ", sourceToConceptMapTable, " does not exist in the vocabularyDatabaseSchema ", vocabularyDatabaseSchema))`
`73`	`73`	`}`