OMOP/tests/testthat/setup.R

115 lines
4.5 KiB
R

# Specify desired test platforms
cdmVersion <- "5.4"
testDatabases <- c("postgresql")
# Download the JDBC drivers used in the tests
library(DatabaseConnector)
missingJarFolderEnvironmentVariable <- FALSE
emptyJarFolderEnivornmentVariable <- FALSE
jarFolderDoesNotExist <- FALSE
missingJarFolderEnvironmentVariable <- is.na(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))
if (missingJarFolderEnvironmentVariable) {
cat("DATABASECONNECTOR_JAR_FOLDER environment variable not set.")
} else {
emptyJarFolderEnivornmentVariable <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")==""
if (emptyJarFolderEnivornmentVariable) {
cat("DATABASECONNECTOR_JAR_FOLDER environment variable is empty string")
} else {
jarFolderDoesNotExist <- !dir.exists(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))
if (jarFolderDoesNotExist) {
cat(paste("specified DATABASECONNECTOR_JAR_FOLDER", Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), "does not exist."))
}
}
}
if ( missingJarFolderEnvironmentVariable| emptyJarFolderEnivornmentVariable | jarFolderDoesNotExist) {
driverPath <- tempdir()
cat("\ndownloading drivers\n")
downloadJdbcDrivers("redshift", pathToDriver = driverPath)
downloadJdbcDrivers("postgresql", pathToDriver = driverPath)
downloadJdbcDrivers("oracle", pathToDriver = driverPath)
downloadJdbcDrivers("sql server", pathToDriver = driverPath)
} else {
driverPath <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
}
# Helper functions used in tests
getConnectionDetails <- function(dbms) {
switch (dbms,
"postgresql" = createConnectionDetails(
dbms = "postgresql",
user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
pathToDriver = driverPath
),
"redshift" = createConnectionDetails(
dbms = "redshift",
user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"),
password = Sys.getenv("CDMDDLBASE_REDSHIFT_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_REDSHIFT_SERVER"),
pathToDriver = driverPath
),
"sql server" = createConnectionDetails(
dbms = "sql server",
user = Sys.getenv("CDMDDLBASE_SQL_SERVER_USER"),
password = Sys.getenv("CDMDDLBASE_SQL_SERVER_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_SQL_SERVER_SERVER"),
pathToDriver = driverPath
),
"oracle" = createConnectionDetails(
dbms = "oracle",
user = Sys.getenv("CDMDDLBASE_ORACLE_USER"),
password = Sys.getenv("CDMDDLBASE_ORACLE_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_ORACLE_SERVER"),
pathToDriver = driverPath
)
)
}
getSchema <- function(dbms) {
switch (dbms,
"postgresql" = Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA"),
"redshift" = Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA"),
"sql server" = Sys.getenv("CDMDDLBASE_SQL_SERVER_CDM_SCHEMA"),
"oracle" = Sys.getenv("CDMDDLBASE_ORACLE_CDM_SCHEMA")
)
}
listTablesInSchema <- function(connectionDetails, schema) {
stopifnot("ConnectionDetails" %in% class(connectionDetails), class(schema) == "character", length(schema) == 1)
stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle"))
con <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(con))
dbms <- connectionDetails$dbms
if(dbms %in% c("postgresql", "redshift", "sql server")) {
tables <- dbGetQuery(con, paste0("select table_name from information_schema.tables where table_schema = '", schema, "'"))[[1]]
} else if(dbms == "oracle") {
query <- paste0("select table_name from all_tables where owner = '", toupper(schema), "' and tablespace_name = 'USERS'")
tables <- dbGetQuery(con, query)[[1]]
}
return(tables)
}
dropAllTablesFromSchema <- function(connectionDetails, schema) {
stopifnot("ConnectionDetails" %in% class(connectionDetails), class(schema) == "character", length(schema) == 1)
stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle"))
tableNames <- listTablesInSchema(connectionDetails, schema)
con <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(con))
dbms <- connectionDetails$dbms
if(dbms %in% c("redshift", "postgresql", "sql server")) {
for(tableName in tableNames) {
DBI::dbExecute(con, paste("DROP TABLE IF EXISTS",paste(schema, tableName, sep = "."),"CASCADE"))
}
} else if(dbms == "oracle") {
for(tableName in tableNames) {
DBI::dbExecute(con, paste("DROP TABLE IF EXISTS",tableName,"CASCADE"))
}
}
}