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Extend unit tests to cover InterSystems IRIS
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,128 +1,136 @@ | ||
| testDatabases <- c("postgresql") | ||
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|
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| if (Sys.getenv("CDM5_POSTGRESQL_SERVER") != "") { | ||
| library(DatabaseConnector) | ||
|
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| 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) | ||
|
|
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| Sys.setenv(DATABASECONNECTOR_JAR_FOLDER = jdbcDriverFolder) | ||
|
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| withr::defer({ | ||
| unlink(jdbcDriverFolder, | ||
| recursive = TRUE, | ||
| force = TRUE) | ||
| }, | ||
| testthat::teardown_env()) | ||
| } | ||
| } 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 | ||
| ) | ||
| 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")) | ||
| } | ||
| } | ||
| } | ||
| 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()) | ||
| } | ||
| } 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 | ||
| ), | ||
| "iris" = createConnectionDetails( | ||
| dbms = "iris", | ||
| user = Sys.getenv("CDMDDLBASE_IRIS_USER"), | ||
| password = Sys.getenv("CDMDDLBASE_IRIS_PASSWORD"), | ||
| connectionString = Sys.getenv("CDMDDLBASE_IRIS_URL"), | ||
| 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"), | ||
| "iris" = Sys.getenv("CDMDDLBASE_IRIS_CDM_SCHEMA") | ||
| ) | ||
| } | ||
|
|
||
| listTablesInSchema <- function(connectionDetails, schema) { | ||
| stopifnot( | ||
| "ConnectionDetails" %in% class(connectionDetails), | ||
| class(schema) == "character", | ||
| length(schema) == 1 | ||
| ) | ||
| stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle", "iris")) | ||
| con <- DatabaseConnector::connect(connectionDetails) | ||
| on.exit(DatabaseConnector::disconnect(con)) | ||
| dbms <- connectionDetails$dbms | ||
| if (dbms %in% c("postgresql", "redshift", "sql server", "iris")) { | ||
| 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$dbms %in% c("postgresql", "redshift", "sql server", "oracle", "iris")) | ||
| tableNames <- listTablesInSchema(connectionDetails, schema) | ||
|
|
||
| con <- DatabaseConnector::connect(connectionDetails) | ||
| on.exit(DatabaseConnector::disconnect(con)) | ||
| dbms <- connectionDetails$dbms | ||
| if (dbms %in% c("redshift", "postgresql", "sql server", "iris")) { | ||
| 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")) | ||
| } | ||
| } | ||
| } |