Add tests for oracle and sql server. Move setup.R file.
This commit is contained in:
Adam Black
parent
2b0acc8d53
commit
cedf334df6
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# Download the JDBC drivers used in the tests
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library(DatabaseConnector)
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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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if(Sys.getenv("LOCAL_TEST") != "TRUE") {
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cat("downloading drivers")
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downloadJdbcDrivers("all", pathToDriver = driverPath)
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}
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postgresDetails <- 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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cdmSchema = Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA")
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)
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redshiftDetails <- 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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cdmSchema = Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA")
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)
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sqlserverDetails <- createConnectionDetails(
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dbms = "sql server",
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user = Sys.getenv("CDMDDLBASE_SQL_SERVER_USER"),
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password = Sys.getenv("CDMDDLBASE_SQL_SERVER_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_SQL_SERVER_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers"),
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cdmSchema = Sys.getenv("CDMDDLBASE_SQL_SERVER_CDM_SCHEMA")
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)
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oracleDetails <- createConnectionDetails(
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dbms = "oracle",
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user = Sys.getenv("CDMDDLBASE_ORACLE_USER"),
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password = Sys.getenv("CDMDDLBASE_ORACLE_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_ORACLE_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers"),
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cdmSchema = Sys.getenv("CDMDDLBASE_ORACLE_CDM_SCHEMA")
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)
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# Download the JDBC drivers used in the tests
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library(DatabaseConnector)
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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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if(Sys.getenv("LOCAL_TEST") != "TRUE") {
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cat("downloading drivers")
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downloadJdbcDrivers("all", pathToDriver = driverPath)
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}
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# Helper functions used in tests -----------------------------------------------
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getConnectionDetails <- function(dbms) {
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switch (dbms,
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"postgresql" = 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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"redshift" = 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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"sql server" = createConnectionDetails(
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dbms = "sql server",
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user = Sys.getenv("CDMDDLBASE_SQL_SERVER_USER"),
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password = Sys.getenv("CDMDDLBASE_SQL_SERVER_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_SQL_SERVER_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
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),
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"oracle" = createConnectionDetails(
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dbms = "oracle",
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user = Sys.getenv("CDMDDLBASE_ORACLE_USER"),
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password = Sys.getenv("CDMDDLBASE_ORACLE_PASSWORD"),
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server = Sys.getenv("CDMDDLBASE_ORACLE_SERVER"),
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pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
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)
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)
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}
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getSchema <- function(dbms) {
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switch (dbms,
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"postgresql" = Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA"),
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"redshift" = Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA"),
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"sql server" = Sys.getenv("CDMDDLBASE_SQL_SERVER_CDM_SCHEMA"),
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"oracle" = Sys.getenv("CDMDDLBASE_ORACLE_CDM_SCHEMA")
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)
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}
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listTablesInSchema <- function(connectionDetails, schema) {
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stopifnot(class(connectionDetails) == "connectionDetails", class(schema) == "character", length(schema) == 1)
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con <- DatabaseConnector::connect(connectionDetails)
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on.exit(DatabaseConnector::disconnect(con))
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dbms <- connectionDetails$dbms
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if(dbms %in% c("postgresql", "redshift", "sql server")) {
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tables <- dbGetQuery(con, paste0("select table_name from information_schema.tables where table_schema = '", schema, "'"))[[1]]
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} else if(dbms == "oracle") {
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query <- paste0("select table_name from all_tables where owner = '", toupper(schema), "' and tablespace_name = 'USERS'")
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tables <- dbGetQuery(con, query)[[1]]
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}
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return(tables)
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}
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dropAllTablesFromSchema <- function(connectionDetails, schema) {
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stopifnot(class(connectionDetails) == "connectionDetails", class(schema) == "character", length(schema) == 1)
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tables <- listTablesInSchema(connectionDetails, schema)
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con <- DatabaseConnector::connect(connectionDetails)
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on.exit(DatabaseConnector::disconnect(con))
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dbms <- connectionDetails$dbms
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if(dbms %in% c("redshift", "postgresql", "sql server")) {
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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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} else if(dbms == "oracle") {
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for(table in tables) {
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DBI::dbRemoveTable(con, name = table)
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}
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}
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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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#
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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$sql), collapse = "")
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# executeSql(con, sql)
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#
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# disconnect(con)
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#
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# }
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@ -1,126 +1,50 @@
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library(DatabaseConnector)
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# To run tests for one dbms and one cdmVersion use the variables below
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# dbms <- "postgresql"; cdmVersion <- "5.4"
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# Helper functions used in tests
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testDatabases <- c("oracle", "postgresql", "sql server", "redshift")
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.listTablesInSchema <- function(connectionDetails, schema) {
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con <- DatabaseConnector::connect(connectionDetails)
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tables <- DBI::dbListObjects(con, prefix = schema)
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DatabaseConnector::disconnect(con)
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test_that("getConnectionDetails works", {
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tables <- subset(tables, is_prefix == FALSE)
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for(dbms in testDatabases) {
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tables <- subset(tables, grepl("table", table))$table
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expect_s3_class(getConnectionDetails(dbms), "connectionDetails")
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tables <- vapply(tables, function(.) .@name, FUN.VALUE = character(1))
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return(tables)
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}
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.dropAllTablesFromSchema <- function(connectionDetails, schema) {
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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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}
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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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#
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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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test_that("Execute DDL on Postgres", {
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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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expect_error(con <- connect(connectionDetails), NA)
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disconnect(con)
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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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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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})
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})
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test_that("Execute DDL on Redshift", {
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test_that("getSchema works", {
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for(dbms in testDatabases) {
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expect_type(getSchema(dbms), "character")
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}
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})
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connectionDetails <- createConnectionDetails(
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for(dbms in testDatabases) {
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dbms = "redshift",
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connectionDetails <- getConnectionDetails(dbms)
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user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"),
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cdmDatabaseSchema <- getSchema(dbms)
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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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test_that(paste("Can connect to", dbms), {
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disconnect(con)
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expect_error(con <- connect(connectionDetails), NA)
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disconnect(con)
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})
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cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA")
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for(cdmVersion in listSupportedVersions()) {
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for(cdmVersion in listSupportedVersions()) {
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# make sure the schema is cleared out
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test_that(paste("DDL", cdmVersion, "runs on", dbms), {
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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executeDdl(connectionDetails,
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tables <- listTablesInSchema(connectionDetails, cdmDatabaseSchema)
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cdmVersion = cdmVersion,
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expect_equal(tables, character(0))
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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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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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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tables <- listTablesInSchema(connectionDetails, cdmDatabaseSchema)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
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# check that the tables in the database match the tables in the specification
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# 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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expect_equal(sort(tolower(tables)), sort(tolower(tableSpecs)))
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dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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# clear schema
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})
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.dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
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}
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}
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}
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})
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