allow to test multiple dbms

closes #48
OHDSI · Jul 29, 2024 · 32af7e7 · 32af7e7
1 parent 29df430
commit 32af7e7
Show file tree

Hide file tree

Showing 4 changed files with 50 additions and 33 deletions.
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -9,3 +9,26 @@ if (!on_cran()) {
   )
   CDMConnector::downloadEunomiaData(overwrite = TRUE)
 }
+connection <- function(type = Sys.getenv("DB_TO_TEST", "duckdb")) {
+  switch(
+    type,
+    "duckdb" = DBI::dbConnect(duckdb::duckdb(), ":memory:")
+  )
+}
+schema <- function(type = Sys.getenv("DB_TO_TEST", "duckdb")) {
+  switch(
+    type,
+    "duckdb" = c(schema = "main", prefix = "os_")
+  )
+}
+cdmEunomia <- function() {
+  con <- connection()
+  schema <- schema()
+  conDuck <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
+  cdmDuck <- CDMConnector::cdmFromCon(
+    con = conDuck, cdmSchema = "main", writeSchema = "main"
+  )
+  cdm <- CDMConnector::copyCdmTo(con = con, cdm = cdmDuck, schema = schema)
+  CDMConnector::cdmDisconnect(cdm = cdmDuck)
+  return(cdm)
+}
diff --git a/tests/testthat/test-summariseClinicalRecords.R b/tests/testthat/test-summariseClinicalRecords.R
@@ -1,10 +1,7 @@
 test_that("summariseClinicalRecords() works", {
 
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
+  cdm <- cdmEunomia()
 
   # Check all tables work ----
   expect_true(inherits(summariseClinicalRecords(cdm$observation_period),"summarised_result"))
@@ -58,20 +55,19 @@ test_that("summariseClinicalRecords() works", {
                                  domainId = FALSE,
                                  typeConcept = FALSE) |>
                 dplyr::tally() |> dplyr::pull() == 3)
-})
 
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
 
 test_that("tableClinicalRecords() works", {
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
+  cdm <- cdmEunomia()
 
   # Check that works ----
   expect_no_error(x <- tableClinicalRecords(summariseClinicalRecords(cdm$condition_occurrence)))
   expect_true(inherits(x,"gt_tbl"))
   expect_warning(t <- summariseClinicalRecords(cdm$death))
   expect_warning(inherits(tableClinicalRecords(t),"gt_tbl"))
-})
 
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
diff --git a/tests/testthat/test-summariseObservationPeriod.R b/tests/testthat/test-summariseObservationPeriod.R
@@ -1,10 +1,7 @@
 test_that("check summariseObservationPeriod works", {
-#
-#   # Load mock database ----
-#   con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-#   cdm <- CDMConnector::cdmFromCon(
-#     con = con, cdmSchema = "main", writeSchema = "main"
-#   )
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
 #
 #   # Check all tables work ----
 #   expect_true(inherits(summariseObservationPeriod(cdm$observation_period),"summarised_result"))
@@ -94,4 +91,6 @@ test_that("check summariseObservationPeriod works", {
 #   expect_true(inherits(plotObservationPeriod(x),"ggplot"))
 #   x <-  x |> dplyr::filter(result_id == -1)
 #   expect_warning(plotObservationPeriod(x))
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
 })
diff --git a/tests/testthat/test-summariseRecordCount.R b/tests/testthat/test-summariseRecordCount.R
@@ -1,10 +1,7 @@
 test_that("summariseRecordCount() works", {
 
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
+  cdm <- cdmEunomia()
 
   # Check inputs ----
   expect_true(inherits(summariseRecordCount(omopTable = cdm$observation_period, unit = "month"),"summarised_result"))
@@ -74,24 +71,26 @@ test_that("summariseRecordCount() works", {
          dplyr::tally() |>
          dplyr::pull("n"))
   )
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
 })
 
 test_that("plotRecordCount() works", {
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
-  expect_true(inherits(plotRecordCount(summariseRecordCount(cdm$drug_exposure, unitInterval = 8)),"ggplot"))
+  cdm <- cdmEunomia()
+
+  p <- summariseRecordCount(cdm$drug_exposure, unitInterval = 8) |>
+    plotRecordCount()
+
+  expect_true(inherits(p,"ggplot"))
   # expect_warning(inherits(plotRecordCount(summariseRecordCount(cdm$death, unitInterval = 8)),"ggplot"))
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
 })
 
 test_that("summariseRecordCount() ageGroup argument works", {
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
+  cdm <- cdmEunomia()
 
   # Check that works ----
   expect_no_error(t <- summariseRecordCount(cdm$condition_occurrence, ageGroup = list(">=65" = c(65, Inf), "<65" = c(0,64))))
@@ -140,15 +139,13 @@ test_that("summariseRecordCount() ageGroup argument works", {
     dplyr::pull(n)
   expect_equal(x,y)
 
+  PatientProfiles::mockDisconnect(cdm = cdm)
 })
 
 
 test_that("summariseRecordCount() sex argument works", {
   # Load mock database ----
-  con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir())
-  cdm <- CDMConnector::cdmFromCon(
-    con = con, cdmSchema = "main", writeSchema = "main"
-  )
+  cdm <- cdmEunomia()
 
   # Check that works ----
   expect_no_error(t <- summariseRecordCount(cdm$condition_occurrence, sex = TRUE))
@@ -197,6 +194,8 @@ test_that("summariseRecordCount() sex argument works", {
     dplyr::pull(n) |>
     as.character()
   expect_equal(x,y)
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
 })