check if tables have been created in the cdm

OHDSI · Dec 20, 2024 · 12086dc · 12086dc
1 parent c297a86
commit 12086dc
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diff --git a/R/summariseObservationPeriod.R b/R/summariseObservationPeriod.R
@@ -123,6 +123,8 @@ summariseObservationPeriod <- function(observationPeriod,
     ) |>
     omopgenerics::newSummarisedResult(settings = set)
 
+  omopgenerics::dropSourceTable(cdm, name = dplyr::starts_with(tablePrefix))
+
   return(obsSr)
 }
 
@@ -204,5 +206,6 @@ arrangeSr <- function(x, estimates) {
     dplyr::left_join(order, by = c("variable_name", "group_level", "strata_level", "estimate_name")) |>
     dplyr::arrange(.data$order_id) |>
     dplyr::select(-"order_id")
+
   return(x)
 }
diff --git a/tests/testthat/test-summariseAllConceptCounts.R b/tests/testthat/test-summariseAllConceptCounts.R
@@ -113,5 +113,30 @@ test_that("tableAllConceptCounts() works", {
   expect_warning(t <- summariseAllConceptCounts(cdm, "death"))
   expect_warning(inherits(tableAllConceptCounts(t),"gt_tbl"))
 
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseAllConceptCounts(cdm = cdm,
+                                       omopTableName = c("drug_exposure", "condition_occurrence"),
+                                       countBy = c("record", "person"),
+                                       year=TRUE,
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")),
+                                       sample = 100)
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
diff --git a/tests/testthat/test-summariseClinicalRecords.R b/tests/testthat/test-summariseClinicalRecords.R
@@ -314,3 +314,26 @@ test_that("summariseClinicalRecords() works with mock data", {
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
 
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseClinicalRecords(cdm = cdm,
+                                       omopTableName = c("drug_exposure", "condition_occurrence"),
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")),
+                                       sample = 100)
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
diff --git a/tests/testthat/test-summariseInObservation.R b/tests/testthat/test-summariseInObservation.R
@@ -274,3 +274,28 @@ test_that("dateRange argument works", {
   expect_equal(colnames(settings(z)), colnames(settings(x)))
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseInObservation(cdm$observation_period,
+                                       output = c("records", "person-days"),
+                                       interval = "years",
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")))
+
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+
diff --git a/tests/testthat/test-summariseMissingData.R b/tests/testthat/test-summariseMissingData.R
@@ -130,3 +130,29 @@ test_that("col not present in table", {
 
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseMissingData(cdm = cdm,
+                                       omopTableName = c("drug_exposure", "condition_occurrence"),
+                                       year=TRUE,
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")),
+                                       sample = 100)
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+
diff --git a/tests/testthat/test-summariseObservationPeriod.R b/tests/testthat/test-summariseObservationPeriod.R
@@ -489,6 +489,30 @@ test_that("dateRnge argument works", {
 
 
 
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+
+
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseObservationPeriod(cdm$observation_period,
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")))
+
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
 
diff --git a/tests/testthat/test-summariseRecordCount.R b/tests/testthat/test-summariseRecordCount.R
@@ -319,3 +319,29 @@ test_that("sample argument works", {
   expect_equal(y,z)
   PatientProfiles::mockDisconnect(cdm = cdm)
 })
+
+test_that("no tables created", {
+  skip_on_cran()
+  # Load mock database ----
+  cdm <- cdmEunomia()
+
+  startNames <- CDMConnector::listSourceTables(cdm)
+
+  results <- summariseRecordCount(cdm = cdm,
+                                       omopTableName = c("drug_exposure", "condition_occurrence"),
+                                       interval = "years",
+                                       sex = TRUE,
+                                       ageGroup = list(c(0,17),
+                                                       c(18,65),
+                                                       c(66, 100)),
+                                       dateRange = as.Date(c("2012-01-01", "2018-01-01")),
+                                       sample = 100)
+
+  endNames <- CDMConnector::listSourceTables(cdm)
+
+  expect_true(length(setdiff(endNames, startNames)) == 0)
+
+
+  PatientProfiles::mockDisconnect(cdm = cdm)
+})
+