OMOP/tests/testthat/test-executeDdl.R

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# connection based tests required environment variables be configured
test_that("CommonDataModel Execution Test", {
if (Sys.getenv("CDM5_POSTGRESQL_SERVER") != "") {
test_that("getConnectionDetails works", {
for (dbms in testDatabases) {
expect_s3_class(getConnectionDetails(dbms), "ConnectionDetails")
}
})
test_that("getSchema works", {
for (dbms in testDatabases) {
expect_type(getSchema(dbms), "character")
}
})
for (dbms in testDatabases) {
connectionDetails <- getConnectionDetails(dbms)
cdmDatabaseSchema <- getSchema(dbms)
test_that(paste("Can connect to", dbms), {
expect_error(con <- connect(connectionDetails), NA)
expect_error(disconnect(con), NA)
})
for (cdmVersion in listSupportedVersions()) {
test_that(paste("DDL", cdmVersion, "runs on", dbms), {
dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
tables <-
listTablesInSchema(connectionDetails, cdmDatabaseSchema)
expect_equal(tables, character(0))
executeDdl(
connectionDetails,
cdmVersion = cdmVersion,
cdmDatabaseSchema = cdmDatabaseSchema,
executeDdl = TRUE,
executePrimaryKey = TRUE,
executeForeignKey = FALSE
)
tables <-
listTablesInSchema(connectionDetails, cdmDatabaseSchema)
cdmTableCsvLoc <-
system.file(file.path(
"csv",
paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")
),
package = "CommonDataModel",
mustWork = TRUE)
tableSpecs <-
read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
# check that the tables in the database match the tables in the specification
expect_equal(sort(tolower(tables)), sort(tolower(tableSpecs)))
dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
})
}
}
} else {
message("Skipping driver setup because environmental variables not set")
}
})