Merge pull request #379 from OHDSI/check_index

Fix bug when reason clumn name for entry/exit is already in cohort
OHDSI · Nov 1, 2024 · 9c1d98f · 9c1d98f
2 parents d5c7305 + b3d49b8
commit 9c1d98f
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Showing 4 changed files with 17 additions and 3 deletions.
diff --git a/R/exitAtColumnDate.R b/R/exitAtColumnDate.R
@@ -125,6 +125,13 @@ exitAtColumnDate <- function(cohort,
     reason <- "entry_reason"
   }
 
+  if (reason %in% colnames(cohort) & returnReason) {
+    cli::cli_inform("Column {reason} will be overwritten.")
+    cohort <- cohort |> dplyr::select(!dplyr::all_of(reason))
+  } else if (reason %in% colnames(cohort) & !returnReason) {
+    reason <- "date_column_name_1234"
+  }
+
   # check NA
   checkNA <- cohort |>
     dplyr::filter(dplyr::if_all(

diff --git a/tests/testthat/test-entryAtColumnDate.R b/tests/testthat/test-entryAtColumnDate.R
@@ -169,7 +169,7 @@ test_that("test indexes - postgres", {
                                                       cohort_end_date = as.Date("2009-01-03"),
                                                       other_date = as.Date("2009-01-01")))
   cdm$my_cohort <- omopgenerics::newCohortTable(cdm$my_cohort)
-  cdm$my_cohort <- entryAtFirstDate(cdm$my_cohort, dateColumns = c("cohort_end_date", "other_date"), returnReason = FALSE)
+  cdm$my_cohort <- entryAtFirstDate(cdm$my_cohort, dateColumns = c("cohort_end_date", "other_date"), returnReason = TRUE)
 
   expect_true(
     DBI::dbGetQuery(db, paste0("SELECT * FROM pg_indexes WHERE tablename = 'cc_my_cohort';")) |> dplyr::pull("indexdef") ==

diff --git a/tests/testthat/test-exitAtColumnDate.R b/tests/testthat/test-exitAtColumnDate.R
@@ -237,14 +237,14 @@ test_that("test indexes - postgres", {
                                                       cohort_end_date = as.Date("2009-01-03"),
                                                       other_date = as.Date("2009-01-01")))
   cdm$my_cohort <- omopgenerics::newCohortTable(cdm$my_cohort)
-  cdm$my_cohort <- exitAtLastDate(cdm$my_cohort, dateColumns = c("cohort_end_date", "other_date"), returnReason = FALSE)
+  cdm$my_cohort <- exitAtLastDate(cdm$my_cohort, dateColumns = c("cohort_end_date", "other_date"), returnReason = TRUE)
 
   expect_true(
     DBI::dbGetQuery(db, paste0("SELECT * FROM pg_indexes WHERE tablename = 'cc_my_cohort';")) |> dplyr::pull("indexdef") ==
       "CREATE INDEX cc_my_cohort_subject_id_cohort_start_date_idx ON public.cc_my_cohort USING btree (subject_id, cohort_start_date)"
   )
 
-  cdm$my_cohort <- exitAtFirstDate(cdm$my_cohort, dateColumns = c("cohort_start_date", "cohort_end_date"), returnReason = FALSE)
+  cdm$my_cohort <- exitAtFirstDate(cdm$my_cohort, dateColumns = c("cohort_start_date", "cohort_end_date"), returnReason = TRUE)
 
   expect_true(
     DBI::dbGetQuery(db, paste0("SELECT * FROM pg_indexes WHERE tablename = 'cc_my_cohort';")) |> dplyr::pull("indexdef") ==

diff --git a/tests/testthat/test-requireIsEntry.R b/tests/testthat/test-requireIsEntry.R
@@ -246,6 +246,12 @@ test_that("test indexes - postgres", {
       "CREATE INDEX cc_my_cohort_subject_id_cohort_start_date_idx ON public.cc_my_cohort USING btree (subject_id, cohort_start_date)"
   )
 
+  cdm$my_cohort <- requireIsEntry(cdm$my_cohort, entryRange = c(1,Inf))
+  expect_true(
+    DBI::dbGetQuery(db, paste0("SELECT * FROM pg_indexes WHERE tablename = 'cc_my_cohort';")) |> dplyr::pull("indexdef") ==
+      "CREATE INDEX cc_my_cohort_subject_id_cohort_start_date_idx ON public.cc_my_cohort USING btree (subject_id, cohort_start_date)"
+  )
+
   cdm$my_cohort <- requireIsFirstEntry(cdm$my_cohort)
   expect_true(
     DBI::dbGetQuery(db, paste0("SELECT * FROM pg_indexes WHERE tablename = 'cc_my_cohort';")) |> dplyr::pull("indexdef") ==
@@ -258,5 +264,6 @@ test_that("test indexes - postgres", {
       "CREATE INDEX cc_my_cohort_subject_id_cohort_start_date_idx ON public.cc_my_cohort USING btree (subject_id, cohort_start_date)"
   )
 
+  omopgenerics::dropTable(cdm = cdm, name = dplyr::starts_with("my_cohort"))
   CDMConnector::cdm_disconnect(cdm = cdm)
 })