test on duckdb on github

darwin-eu · Dec 9, 2023 · 1ee48e0 · 1ee48e0
1 parent abe0de2
commit 1ee48e0
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Showing 3 changed files with 76 additions and 12 deletions.
diff --git a/.github/workflows/duckdb-test.yaml b/.github/workflows/duckdb-test.yaml
@@ -0,0 +1,60 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Postgres-test
+
+jobs:
+  R-CMD-check:
+    if: github.repository == 'darwin-eu/CDMConnector' || github.repository == 'darwin-eu-dev/CDMConnector'
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: true
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install suggested packages
+        run: |
+            install.packages("DatabaseConnector")
+            install.packages("RPostgres")
+            install.packages("testthat")
+        shell: Rscript {0}
+
+      - name: Install CirceR
+        run: |
+            install.packages("rJava")
+            install.packages("RJSONIO")
+            install.packages("CirceR", repos = "https://OHDSI.github.io/drat", type = "source")
+            install.packages("Capr", repos = "https://OHDSI.github.io/drat", type = "source")
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      -  name: Run tests on duckdb
+         run: |
+            withr::with_envvar(new = c("CI_TEST_DB" = "duckdb"), testthat::test_local())
+         shell: Rscript {0}
+
+
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -102,7 +102,7 @@ get_cdm_schema <- function(dbms) {
   return(s)
 }
 
-get_write_schema <- function(dbms, prefix = NULL) {
+get_write_schema <- function(dbms, prefix = paste0("temp", as.integer(Sys.time()) %% 10000L, "_")) {
   s <- switch (dbms,
           "postgres" = Sys.getenv("CDM5_POSTGRESQL_SCRATCH_SCHEMA"),
           "local" = Sys.getenv("LOCAL_POSTGRESQL_SCRATCH_SCHEMA"),
@@ -158,5 +158,7 @@ if (Sys.getenv("CI_TEST_DB") == "") {
   checkmate::assert_choice(Sys.getenv("CI_TEST_DB"),
                            choices = c("duckdb", "postgres", "sqlserver", "redshift"))
   dbToTest <- Sys.getenv("CI_TEST_DB")
-  print(paste("running tests. on ", dbToTest))
+  print(paste("running CI tests on ", dbToTest))
 }
+
+
diff --git a/tests/testthat/test-db-cohort_ddl.R b/tests/testthat/test-db-cohort_ddl.R
@@ -1,30 +1,32 @@
 test_cohort_ddl <- function(con, write_schema) {
+  skip_if_not("prefix" %in% names(write_schema))
+  name <- "testcohort"
+
   expect_no_error(
     createCohortTables(con,
                        writeSchema = write_schema,
-                       name = "testcohort",
+                       name = name,
                        computeAttrition = FALSE)
   )
 
   tables <- sort(list_tables(con, schema = write_schema))
 
-  # cleanup ...
-  # tables_to_drop <- tables %>% stringr::str_subset("TEST")
-  # purrr::walk(tables_to_drop, ~DBI::dbRemoveTable(con, inSchema(write_schema , .)))
-
-  name <- paste0(tidyr::replace_na(write_schema["prefix"], ""), "testcohort")
-
   if (dbms(con) %in% c("oracle", "snowflake")) {
     name <- toupper(name)
   }
 
   expect_true(name %in% tables)
 
-  if ("prefix" %in% names(write_schema)) {
-    write_schema <- unname(write_schema[names(write_schema) != "prefix"])
+  tables_to_drop <- stringr::str_subset(tables, name)
+
+  for (tb in tables_to_drop) {
+    DBI::dbRemoveTable(con, inSchema(write_schema, tb, dbms = dbms(con)))
   }
 
-  DBI::dbRemoveTable(con, inSchema(write_schema, name, dbms = dbms(con)))
+  tables <- list_tables(con, schema = write_schema)
+  for (tb in tables_to_drop) {
+    expect_false(tb %in% tables)
+  }
 }
 
 for (dbtype in dbToTest) {