tests/testthat/setup.R

In quinterpriest/FeatureExtraction: Generating Features for a Cohort

# Download the JDBC drivers used in the tests

oldJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = tempfile("jdbcDrivers"))
downloadJdbcDrivers("postgresql")
downloadJdbcDrivers("sql server")
downloadJdbcDrivers("oracle")

withr::defer({
  unlink(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), recursive = TRUE, force = TRUE)
  Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = oldJarFolder)
}, testthat::teardown_env())

getTestResourceFilePath <- function(fileName) {
  return(system.file("testdata", fileName, package = "FeatureExtraction"))
}

# Use this instead of SqlRender directly to avoid errors when running 
# individual test files
loadRenderTranslateSql <- function(sqlFileName, targetDialect, tempEmulationSchema = NULL, ...) {
  sql <- SqlRender::readSql(system.file("sql/sql_server/", sqlFileName, package = "FeatureExtraction"))
  sql <- SqlRender::render(sql = sql, ...)
  sql <- SqlRender::translate(sql = sql, targetDialect = targetDialect, tempEmulationSchema = tempEmulationSchema)
  return(sql)
}

# Get all environment variables to determine which DBMS to use for testing
# AGS: Turning off Oracle database-level testing for now
runTestsOnPostgreSQL <- !(Sys.getenv("CDM5_POSTGRESQL_USER") == "" & Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" & Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" & Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" & Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "")
runTestsOnSQLServer <- FALSE #!(Sys.getenv("CDM5_SQL_SERVER_USER") == "" & Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" & Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" & Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" & Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "")
runTestsOnOracle <- FALSE #!(Sys.getenv("CDM5_ORACLE_USER") == "" & Sys.getenv("CDM5_ORACLE_PASSWORD") == "" & Sys.getenv("CDM5_ORACLE_SERVER") == "" & Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" & Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "")
runTestsOnImpala <- FALSE #!(Sys.getenv("CDM5_IMPALA_USER") == "" & Sys.getenv("CDM5_IMPALA_PASSWORD") == "" & Sys.getenv("CDM5_IMPALA_SERVER") == "" & Sys.getenv("CDM5_IMPALA_CDM_SCHEMA") == "" & Sys.getenv("CDM5_IMPALA_OHDSI_SCHEMA") == "")
runTestsOnEunomia <- TRUE