add tests for write and execute functions

tests/testthat/test-executeDdl.R

@@ -0,0 +1,78 @@
+library(DatabaseConnector)
+
+connectionDetails <- createConnectionDetails(
+    dbms = "postgresql",
+    user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
+    password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
+    server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER")
+)
+
+# Helper functions used in tests
+.listTablesInSchema <- function(connectionDetails, schema) {
+  con <- DatabaseConnector::connect(connectionDetails)
+  tables <- DBI::dbListObjects(con, prefix = "cdmddlbase")
+  DatabaseConnector::disconnect(con)
+  tables <- subset(tables, is_prefix == FALSE)
+  tables <- subset(tables, grepl("table", table))$table
+  tables <- vapply(tables, function(.) .@name, FUN.VALUE = character(1))
+  return(tables)
+}
+
+.dropAllTablesFromSchema <- function(connectionDetails, schema) {
+  tables <- .listTablesInSchema(connectionDetails, schema)
+
+  con <- DatabaseConnector::connect(connectionDetails)
+  for(table in tables) {
+    DBI::dbRemoveTable(con, name = DBI::SQL(paste(schema, table, sep = ".")))
+  }
+  DatabaseConnector::disconnect(con)
+}
+
+.removeConstraintsPostgresql <- function(connectionDetails, schema) {
+  # the order of removal of constraints matters!
+  con <- DatabaseConnector::connect(connectionDetails)
+  constraints <- DBI::dbGetQuery(con,
+  "SELECT con.conname, rel.relname as relname
+    FROM pg_catalog.pg_constraint con
+  INNER JOIN pg_catalog.pg_class rel
+  ON rel.oid = con.conrelid
+  INNER JOIN pg_catalog.pg_namespace nsp
+  ON nsp.oid = connamespace
+  WHERE nsp.nspname = 'cdmddlbase';")
+
+
+  constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
+
+  sql <- paste(rev(constraints$sql), collapse = "")
+  executeSql(con, sql)
+
+  disconnect(con)
+
+}
+
+test_that("Execute DDL on Postgres", {
+  # make sure the schema is cleared out
+  cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA")
+  cdmVersion <- "5.4"
+  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
+  .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+  con <- connect(connectionDetails)
+  executeDdl(connectionDetails,
+             cdmVersion = cdmVersion,
+             cdmDatabaseSchema = cdmDatabaseSchema,
+             executeDdl = TRUE,
+             executePrimaryKey = FALSE,
+             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
+  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
+  .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+})

tests/testthat/test-writeDdl.R

@@ -0,0 +1,51 @@
+test_that("writeDdl works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeDdl(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writePrimaryKeys works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writePrimaryKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writeForeignKeys works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeForeignKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writeIndex works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeIndex(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})