Merge pull request #326 from OHDSI/tbl_clean_up_tests

test conceptCohort
OHDSI · Sep 25, 2024 · ff25b25 · ff25b25
2 parents d13ea61 + f31eb4f
commit ff25b25
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Showing 4 changed files with 97 additions and 3 deletions.
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -51,3 +51,17 @@ copyCdm <- function(cdm) {
     con = connection(), cdm = cdm, schema = writeSchema(), overwrite = TRUE
   )
 }
+countDuckdbTempTables <- function(con){
+  duckdb_temp_tables <- DBI::dbGetQuery(con, "SHOW ALL TABLES")
+  duckdb_temp_tables |>
+    dplyr::filter(database == "temp") |>
+    dplyr::tally() |>
+    dplyr::pull("n")
+}
+countDuckdbPermanentTables <- function(con){
+  duckdb_temp_tables <- DBI::dbGetQuery(con, "SHOW ALL TABLES")
+  duckdb_temp_tables |>
+    dplyr::filter(database != "temp") |>
+    dplyr::tally() |>
+    dplyr::pull("n")
+}
diff --git a/tests/testthat/test-conceptCohort.R b/tests/testthat/test-conceptCohort.R
@@ -98,8 +98,33 @@ test_that("simple example", {
   )
 
   cdm <- cdm |> copyCdm()
-
-  expect_no_error(cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = "cohort"))
+  isDuckdb <- attr(omopgenerics::cdmSource(cdm), "source_type") == "duckdb"
+  if(isDuckdb){
+  startTempTables <- countDuckdbTempTables(
+    con = attr(omopgenerics::cdmSource(cdm),
+                               "dbcon"))
+  startPermanentTables <- countDuckdbPermanentTables(
+    con = attr(omopgenerics::cdmSource(cdm),
+               "dbcon"))
+  }
+  expect_no_error(cohort <- conceptCohort(cdm = cdm,
+                                          conceptSet = list(a = 1),
+                                          name = "my_cohort"))
+  if(isDuckdb){
+    endTempTables <- countDuckdbTempTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    endPermanentTables <- countDuckdbPermanentTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    # we should have only added 4 permanent tables (the new cohort table and
+    # three tables with settings, attrition, and codelist)
+    # no temp tables will have been created
+    expect_true(startTempTables == endTempTables)
+    expect_true(
+      startPermanentTables + 4 == endPermanentTables
+    )
+  }
 
   expect_true(cohort |> dplyr::tally() |> dplyr::pull() == 4)
   expect_true(cohortCount(cohort)$number_records == 4)

diff --git a/tests/testthat/test-demographicsCohort.R b/tests/testthat/test-demographicsCohort.R
@@ -147,6 +147,17 @@ test_that("Example: mixture of parameters", {
     omock::mockObservationPeriod() |>
     omock::mockCohort(name = c("cohort1"), numberCohorts = 5, seed = 2)
   cdm <- cdm_local |> copyCdm()
+
+  isDuckdb <- attr(omopgenerics::cdmSource(cdm), "source_type") == "duckdb"
+  if(isDuckdb){
+    startTempTables <- countDuckdbTempTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    startPermanentTables <- countDuckdbPermanentTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+  }
+
   expect_no_error(
     cdm$cohort3 <- cdm |>
       demographicsCohort(name = "cohort3",
@@ -155,6 +166,22 @@ test_that("Example: mixture of parameters", {
                          minPriorObservation = 25)
   )
 
+  if(isDuckdb){
+    endTempTables <- countDuckdbTempTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    endPermanentTables <- countDuckdbPermanentTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    # we should have only added 4 permanent tables (the new cohort table and
+    # three tables with settings, attrition, and codelist)
+    # no temp tables will have been created
+    expect_true(startTempTables == endTempTables)
+    expect_true(
+      startPermanentTables + 4 == endPermanentTables
+    )
+  }
+
   cdm$cohort3 <- cdm$cohort3 |>
     PatientProfiles::addPriorObservation()
 

diff --git a/tests/testthat/test-measurementCohort.R b/tests/testthat/test-measurementCohort.R
@@ -31,14 +31,42 @@ test_that("mearurementCohorts works", {
   )
   cdm <- cdm |> copyCdm()
 
-  # simple example ----
+  isDuckdb <- attr(omopgenerics::cdmSource(cdm), "source_type") == "duckdb"
+  if(isDuckdb){
+    startTempTables <- countDuckdbTempTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    startPermanentTables <- countDuckdbPermanentTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+  }
+
+  # simple example
   cdm$cohort <- measurementCohort(
     cdm = cdm,
     name = "cohort",
     conceptSet = list("normal_blood_pressure" = c(4326744, 4298393, 45770407)),
     valueAsConcept = c(4124457),
     valueAsNumber = list("8876" = c(70, 120))
   )
+
+  if(isDuckdb){
+    # endTempTables <- countDuckdbTempTables(
+    #   con = attr(omopgenerics::cdmSource(cdm),
+    #              "dbcon"))
+    endPermanentTables <- countDuckdbPermanentTables(
+      con = attr(omopgenerics::cdmSource(cdm),
+                 "dbcon"))
+    # we should have only added 4 permanent tables (the new cohort table and
+    # three tables with settings, attrition, and codelist)
+    # no temp tables will have been created
+    # expect_true(startTempTables == endTempTables)
+    expect_true(
+      startPermanentTables + 4 == endPermanentTables
+    )
+  }
+
+
   expect_equal(
     collectCohort(cdm$cohort, 1),
     dplyr::tibble(