OMOP/tests/testthat/setup.R

129 lines
4.0 KiB
R
Raw Normal View History

testDatabases <- c("postgresql")
if (Sys.getenv("CDM5_POSTGRESQL_SERVER") != "") {
library(DatabaseConnector)
if (dir.exists(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))) {
jdbcDriverFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
} else {
jdbcDriverFolder <- file.path(tempdir(), "jdbcDrivers")
dir.create(jdbcDriverFolder, showWarnings = FALSE)
DatabaseConnector::downloadJdbcDrivers("all", pathToDriver = jdbcDriverFolder)
Sys.setenv(DATABASECONNECTOR_JAR_FOLDER = jdbcDriverFolder)
withr::defer({
unlink(jdbcDriverFolder,
recursive = TRUE,
force = TRUE)
},
testthat::teardown_env())
}
2023-09-07 17:52:20 +00:00
} else {
message("Skipping driver setup because environmental variables not set")
}
# 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 = jdbcDriverFolder
),
"redshift" = createConnectionDetails(
dbms = "redshift",
user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"),
password = Sys.getenv("CDMDDLBASE_REDSHIFT_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_REDSHIFT_SERVER"),
pathToDriver = jdbcDriverFolder
),
"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 = jdbcDriverFolder
),
"oracle" = createConnectionDetails(
dbms = "oracle",
user = Sys.getenv("CDMDDLBASE_ORACLE_USER"),
password = Sys.getenv("CDMDDLBASE_ORACLE_PASSWORD"),
server = Sys.getenv("CDMDDLBASE_ORACLE_SERVER"),
pathToDriver = jdbcDriverFolder
)
)
}
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
)
2021-08-20 02:45:23 +00:00
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
)
2021-08-20 02:45:23 +00:00
stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle"))
2023-09-07 17:52:20 +00:00
tableNames <- listTablesInSchema(connectionDetails, schema)
con <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(con))
dbms <- connectionDetails$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"))
}
}
}