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") 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("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 cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA") cdmVersion <- "5.4" # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema) .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema) cat(paste("Connecting to schema", cdmDatabaseSchema, "\n")) 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) })