tests/testthat/test-executeDdl.R

In CommonDataModel: OMOP CDM DDL and Documentation Generator

# connection based tests required environment variables be configured
test_that("CommonDataModel Execution Test", {
  if (Sys.getenv("CDM5_POSTGRESQL_SERVER") != "") {
    test_that("getConnectionDetails works", {
      for (dbms in testDatabases) {
        expect_s3_class(getConnectionDetails(dbms), "ConnectionDetails")
      }
    })

    test_that("getSchema works", {
      for (dbms in testDatabases) {
        expect_type(getSchema(dbms), "character")
      }
    })

    for (dbms in testDatabases) {
      connectionDetails <- getConnectionDetails(dbms)
      cdmDatabaseSchema <- getSchema(dbms)

      test_that(paste("Can connect to", dbms), {
        expect_error(con <- connect(connectionDetails), NA)
        expect_error(disconnect(con), NA)
      })

      for (cdmVersion in listSupportedVersions()) {
        test_that(paste("DDL", cdmVersion, "runs on", dbms), {
          dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
          tables <-
            listTablesInSchema(connectionDetails, cdmDatabaseSchema)
          expect_equal(tables, character(0))

          executeDdl(
            connectionDetails,
            cdmVersion = cdmVersion,
            cdmDatabaseSchema = cdmDatabaseSchema,
            executeDdl = TRUE,
            executePrimaryKey = TRUE,
            executeForeignKey = FALSE
          )

          tables <-
            listTablesInSchema(connectionDetails, 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(tolower(tables)), sort(tolower(tableSpecs)))
          dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
        })
      }
    }
  } else {
    message("Skipping driver setup because environmental variables not set")
  }
})