Add tests for redshift. Clean up test setup file.

R/listSupportedVersions.R

@@ -1,7 +1,7 @@
 #' List CDM versions supported by this package
 #'
+#' @return A character vector containing the support CDM versions in {major}.{minor} format.
 #' @export
-
 listSupportedVersions <- function() {
   supportedVersions <- c("5.3", "5.4")
   return(supportedVersions)

tests/setup.R

@@ -1,21 +1,9 @@
 # Download the JDBC drivers used in the tests
 
-# oldJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
-
 driverPath <- file.path(Sys.getenv("HOME"), "drivers")
 if(!dir.exists(driverPath)) dir.create(driverPath)
-Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = driverPath)
-DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = driverPath)
 
-print(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))
+if(!Sys.getenv("LOCAL_TEST" == "TRUE")) {
-print(list.files(driverPath))
+  DatabaseConnector::downloadJdbcDrivers("all", pathToDriver = driverPath)
-# if(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER") == "") {
+}
-  # driverPath <- file.path(Sys.getenv("HOME"), "drivers")
-# }
-# downloadJdbcDrivers("sql server")
-# downloadJdbcDrivers("oracle")
 
-# withr::defer({
-#   unlink(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), recursive = TRUE, force = TRUE)
-#   Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = oldJarFolder)
-# }, testthat::teardown_env())

tests/testthat/test-executeDdl.R

@@ -1,17 +1,9 @@
 library(DatabaseConnector)
 
-connectionDetails <- createConnectionDetails(
-    dbms = "postgresql",
-    user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
-    password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
-    server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
-    pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
-)
-
 # Helper functions used in tests
 .listTablesInSchema <- function(connectionDetails, schema) {
   con <- DatabaseConnector::connect(connectionDetails)
-  tables <- DBI::dbListObjects(con, prefix = "cdmddlbase")
+  tables <- DBI::dbListObjects(con, prefix = schema)
   DatabaseConnector::disconnect(con)
   tables <- subset(tables, is_prefix == FALSE)
   tables <- subset(tables, grepl("table", table))$table
@@ -29,45 +21,54 @@ connectionDetails <- createConnectionDetails(
   DatabaseConnector::disconnect(con)
 }
 
-.removeConstraintsPostgresql <- function(connectionDetails, schema) {
+# .removeConstraintsPostgresql <- function(connectionDetails, schema) {
-  # the order of removal of constraints matters!
+#   # the order of removal of constraints matters!
-  con <- DatabaseConnector::connect(connectionDetails)
+#   con <- DatabaseConnector::connect(connectionDetails)
-  constraints <- DBI::dbGetQuery(con,
+#   constraints <- DBI::dbGetQuery(con,
-  "SELECT con.conname, rel.relname as relname
+#   "SELECT con.conname, rel.relname as relname
-    FROM pg_catalog.pg_constraint con
+#     FROM pg_catalog.pg_constraint con
-  INNER JOIN pg_catalog.pg_class rel
+#   INNER JOIN pg_catalog.pg_class rel
-  ON rel.oid = con.conrelid
+#   ON rel.oid = con.conrelid
-  INNER JOIN pg_catalog.pg_namespace nsp
+#   INNER JOIN pg_catalog.pg_namespace nsp
-  ON nsp.oid = connamespace
+#   ON nsp.oid = connamespace
-  WHERE nsp.nspname = 'cdmddlbase';")
+#   WHERE nsp.nspname = 'cdmddlbase';")
+#
+#
+#   constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
+#
+#   sql <- paste(rev(constraints$sql), collapse = "")
+#   executeSql(con, sql)
+#
+#   disconnect(con)
+#
+# }
 
 
-  constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
-
-  sql <- paste(rev(constraints$sql), collapse = "")
-  executeSql(con, sql)
-
-  disconnect(con)
-
-}
-
-test_that("Database can be connected to", {
-  expect_error(con <- connect(connectionDetails), NA)
-  disconnect(con)
-})
 
 test_that("Execute DDL on Postgres", {
-  # make sure the schema is cleared out
+
+  connectionDetails <- createConnectionDetails(
+      dbms = "postgresql",
+      user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
+      password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
+      server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
+      pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
+  )
+
   cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA")
-  cdmVersion <- "5.4"
+
-  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
+  expect_error(con <- connect(connectionDetails), NA)
+  disconnect(con)
+
+  for(cdmVersion in listSupportedVersions()) {
+    # make sure the schema is cleared out
     .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
     cat(paste("Connecting to schema", cdmDatabaseSchema, "\n"))
     executeDdl(connectionDetails,
                cdmVersion = cdmVersion,
                cdmDatabaseSchema = cdmDatabaseSchema,
                executeDdl = TRUE,
-             executePrimaryKey = FALSE,
+               executePrimaryKey = TRUE,
                executeForeignKey = FALSE)
 
     tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
@@ -79,6 +80,44 @@ test_that("Execute DDL on Postgres", {
     expect_equal(sort(tables), sort(tableSpecs))
 
     # clear schema
-  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
     .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+  }
+})
+
+test_that("Execute DDL on Redshift", {
+
+  connectionDetails <- createConnectionDetails(
+    dbms = "redshift",
+    user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"),
+    password = Sys.getenv("CDMDDLBASE_REDSHIFT_PASSWORD"),
+    server = Sys.getenv("CDMDDLBASE_REDSHIFT_SERVER"),
+    pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
+  )
+
+  expect_error(con <- connect(connectionDetails), NA)
+  disconnect(con)
+
+  cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA")
+
+  for(cdmVersion in listSupportedVersions()) {
+    # make sure the schema is cleared out
+    .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+    executeDdl(connectionDetails,
+               cdmVersion = cdmVersion,
+               cdmDatabaseSchema = cdmDatabaseSchema,
+               executeDdl = TRUE,
+               executePrimaryKey = TRUE,
+               executeForeignKey = FALSE)
+
+    tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
+
+    cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+    tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
+
+    # check that the tables in the database match the tables in the specification
+    expect_equal(sort(tables), sort(tableSpecs))
+
+    # clear schema
+    .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+  }
 })