Add tests for redshift. Clean up test setup file.
This commit is contained in:
Adam Black
parent
05e9b801e0
commit
ed5fb2d428
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@ -1,7 +1,7 @@
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#' List CDM versions supported by this package
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#'
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#' @return A character vector containing the support CDM versions in {major}.{minor} format.
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#' @export
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listSupportedVersions <- function() {
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supportedVersions <- c("5.3", "5.4")
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return(supportedVersions)
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@ -1,21 +1,9 @@
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# Download the JDBC drivers used in the tests
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# oldJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
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driverPath <- file.path(Sys.getenv("HOME"), "drivers")
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if(!dir.exists(driverPath)) dir.create(driverPath)
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Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = driverPath)
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DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = driverPath)
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print(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))
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print(list.files(driverPath))
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# if(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER") == "") {
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# driverPath <- file.path(Sys.getenv("HOME"), "drivers")
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# }
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# downloadJdbcDrivers("sql server")
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# downloadJdbcDrivers("oracle")
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if(!Sys.getenv("LOCAL_TEST" == "TRUE")) {
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DatabaseConnector::downloadJdbcDrivers("all", pathToDriver = driverPath)
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}
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# withr::defer({
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# unlink(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), recursive = TRUE, force = TRUE)
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# Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = oldJarFolder)
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# }, testthat::teardown_env())
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@ -1,17 +1,9 @@
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library(DatabaseConnector)
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connectionDetails <- createConnectionDetails(
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dbms = "postgresql",
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user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
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password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
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)
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# Helper functions used in tests
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.listTablesInSchema <- function(connectionDetails, schema) {
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con <- DatabaseConnector::connect(connectionDetails)
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tables <- DBI::dbListObjects(con, prefix = "cdmddlbase")
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tables <- DBI::dbListObjects(con, prefix = schema)
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DatabaseConnector::disconnect(con)
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tables <- subset(tables, is_prefix == FALSE)
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tables <- subset(tables, grepl("table", table))$table
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@ -23,62 +15,109 @@ connectionDetails <- createConnectionDetails(
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tables <- .listTablesInSchema(connectionDetails, schema)
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con <- DatabaseConnector::connect(connectionDetails)
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for(table in tables) {
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DBI::dbRemoveTable(con, name = DBI::SQL(paste(schema, table, sep = ".")))
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for(table in tables) {
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DBI::dbRemoveTable(con, name = DBI::SQL(paste(schema, table, sep = ".")))
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}
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DatabaseConnector::disconnect(con)
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}
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.removeConstraintsPostgresql <- function(connectionDetails, schema) {
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# the order of removal of constraints matters!
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con <- DatabaseConnector::connect(connectionDetails)
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constraints <- DBI::dbGetQuery(con,
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"SELECT con.conname, rel.relname as relname
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FROM pg_catalog.pg_constraint con
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INNER JOIN pg_catalog.pg_class rel
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ON rel.oid = con.conrelid
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INNER JOIN pg_catalog.pg_namespace nsp
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ON nsp.oid = connamespace
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WHERE nsp.nspname = 'cdmddlbase';")
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# .removeConstraintsPostgresql <- function(connectionDetails, schema) {
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# # the order of removal of constraints matters!
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# con <- DatabaseConnector::connect(connectionDetails)
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# constraints <- DBI::dbGetQuery(con,
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# "SELECT con.conname, rel.relname as relname
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# FROM pg_catalog.pg_constraint con
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# INNER JOIN pg_catalog.pg_class rel
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# ON rel.oid = con.conrelid
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# INNER JOIN pg_catalog.pg_namespace nsp
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# ON nsp.oid = connamespace
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# WHERE nsp.nspname = 'cdmddlbase';")
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#
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#
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# constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
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#
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# sql <- paste(rev(constraints$sql), collapse = "")
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# executeSql(con, sql)
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#
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# disconnect(con)
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#
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# }
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constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
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sql <- paste(rev(constraints$sql), collapse = "")
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executeSql(con, sql)
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disconnect(con)
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}
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test_that("Database can be connected to", {
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expect_error(con <- connect(connectionDetails), NA)
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disconnect(con)
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})
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test_that("Execute DDL on Postgres", {
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# make sure the schema is cleared out
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connectionDetails <- createConnectionDetails(
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dbms = "postgresql",
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user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
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password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
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)
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cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA")
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cdmVersion <- "5.4"
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# .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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cat(paste("Connecting to schema", cdmDatabaseSchema, "\n"))
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executeDdl(connectionDetails,
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cdmVersion = cdmVersion,
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cdmDatabaseSchema = cdmDatabaseSchema,
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executeDdl = TRUE,
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executePrimaryKey = FALSE,
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executeForeignKey = FALSE)
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tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
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expect_error(con <- connect(connectionDetails), NA)
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disconnect(con)
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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
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for(cdmVersion in listSupportedVersions()) {
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# make sure the schema is cleared out
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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cat(paste("Connecting to schema", cdmDatabaseSchema, "\n"))
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executeDdl(connectionDetails,
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cdmVersion = cdmVersion,
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cdmDatabaseSchema = cdmDatabaseSchema,
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executeDdl = TRUE,
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executePrimaryKey = TRUE,
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executeForeignKey = FALSE)
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# check that the tables in the database match the tables in the specification
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expect_equal(sort(tables), sort(tableSpecs))
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tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
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# clear schema
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# .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
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# check that the tables in the database match the tables in the specification
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expect_equal(sort(tables), sort(tableSpecs))
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# clear schema
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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}
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})
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test_that("Execute DDL on Redshift", {
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connectionDetails <- createConnectionDetails(
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dbms = "redshift",
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user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"),
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password = Sys.getenv("CDMDDLBASE_REDSHIFT_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_REDSHIFT_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
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)
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expect_error(con <- connect(connectionDetails), NA)
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disconnect(con)
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cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA")
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for(cdmVersion in listSupportedVersions()) {
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# make sure the schema is cleared out
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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executeDdl(connectionDetails,
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cdmVersion = cdmVersion,
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cdmDatabaseSchema = cdmDatabaseSchema,
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executeDdl = TRUE,
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executePrimaryKey = TRUE,
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executeForeignKey = FALSE)
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tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
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# check that the tables in the database match the tables in the specification
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expect_equal(sort(tables), sort(tableSpecs))
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# clear schema
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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}
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})
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