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Restore GHA test config
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@anthonysena
anthonysena committed Aug 31, 2023
1 parent 74263f0 commit 2187fda
Showing 1 changed file with 109 additions and 109 deletions.
218 changes: 109 additions & 109 deletions tests/testthat/setup.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,31 +20,31 @@ if (dir.exists(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))) {
dir.create(jdbcDriverFolder, showWarnings = FALSE)
baseDatabaseConnectorJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = jdbcDriverFolder)
# withr::defer(
# {
# unlink(jdbcDriverFolder, recursive = TRUE, force = TRUE)
# Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = baseDatabaseConnectorJarFolder)
# },
# testthat::teardown_env()
# )
withr::defer(
{
unlink(jdbcDriverFolder, recursive = TRUE, force = TRUE)
Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = baseDatabaseConnectorJarFolder)
},
testthat::teardown_env()
)
}


# Create a unique ID for the table identifiers
tableSuffix <- paste0(substr(.Platform$OS.type, 1, 3), format(Sys.time(), "%y%m%d%H%M%S"), sample(1:100, 1))
tableSuffix <- abs(digest::digest2int(tableSuffix))

tempDir <- "D:" #tempfile() #
tempDir <- tempfile() #"D:"
tempDir <- gsub("\\\\", "/", tempDir) # Correct windows path
renvCachePath <- file.path(tempDir, "strategus/renv")
moduleFolder <- file.path(tempDir, "strategus/modules")
Sys.setenv("INSTANTIATED_MODULES_FOLDER" = moduleFolder)
# withr::defer(
# {
# unlink(c(tempDir, renvCachePath, moduleFolder), recursive = TRUE, force = TRUE)
# },
# testthat::teardown_env()
# )
withr::defer(
{
unlink(c(tempDir, renvCachePath, moduleFolder), recursive = TRUE, force = TRUE)
},
testthat::teardown_env()
)

# Assemble a list of connectionDetails for the tests -----------
connectionDetailsList <- list()
Expand Down Expand Up @@ -78,101 +78,101 @@ connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
tempEmulationSchema = NULL
)

# # PostgreSQL
# if (!(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") == "")) {
# DatabaseConnector::downloadJdbcDrivers("postgresql")
# connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
# connectionDetails = DatabaseConnector::createConnectionDetails(
# dbms = "postgresql",
# user = Sys.getenv("CDM5_POSTGRESQL_USER"),
# password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
# server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
# port = 5432,
# pathToDriver = jdbcDriverFolder
# ),
# cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
# workDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
# vocabularyDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
# cohortTable = "cohort",
# tempEmulationSchema = NULL
# )
# }
#
# # Oracle
# if (!(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") == "")) {
# DatabaseConnector::downloadJdbcDrivers("oracle")
# connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
# connectionDetails = DatabaseConnector::createConnectionDetails(
# dbms = "oracle",
# user = Sys.getenv("CDM5_ORACLE_USER"),
# password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
# server = Sys.getenv("CDM5_ORACLE_SERVER"),
# port = 1521,
# pathToDriver = jdbcDriverFolder
# ),
# cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
# workDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
# vocabularyDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
# cohortTable = "cohort",
# tempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA")
# )
# }
#
# # RedShift
# if (!(Sys.getenv("CDM5_REDSHIFT_USER") == ""
# & Sys.getenv("CDM5_REDSHIFT_PASSWORD") == ""
# & Sys.getenv("CDM5_REDSHIFT_SERVER") == ""
# & Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == ""
# & Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")) {
# DatabaseConnector::downloadJdbcDrivers("redshift")
# connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
# connectionDetails = DatabaseConnector::createConnectionDetails(
# dbms = "redshift",
# user = Sys.getenv("CDM5_REDSHIFT_USER"),
# password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
# server = Sys.getenv("CDM5_REDSHIFT_SERVER"),
# port = 5439,
# pathToDriver = jdbcDriverFolder
# ),
# cdmDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
# workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
# vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
# cohortTable = "cohort",
# tempEmulationSchema = NULL
# )
# }
#
# # SQL Server
# if (!(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") == "")) {
# DatabaseConnector::downloadJdbcDrivers("sql server")
# connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
# connectionDetails = DatabaseConnector::createConnectionDetails(
# dbms = "sql server",
# user = Sys.getenv("CDM5_SQL_SERVER_USER"),
# password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
# server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
# port = 1433,
# pathToDriver = jdbcDriverFolder
# ),
# cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
# workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
# vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
# cohortTable = "cohort",
# tempEmulationSchema = NULL
# )
# }
# PostgreSQL
if (!(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") == "")) {
DatabaseConnector::downloadJdbcDrivers("postgresql")
connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
connectionDetails = DatabaseConnector::createConnectionDetails(
dbms = "postgresql",
user = Sys.getenv("CDM5_POSTGRESQL_USER"),
password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
port = 5432,
pathToDriver = jdbcDriverFolder
),
cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
workDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
vocabularyDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
cohortTable = "cohort",
tempEmulationSchema = NULL
)
}

# Oracle
if (!(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") == "")) {
DatabaseConnector::downloadJdbcDrivers("oracle")
connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
connectionDetails = DatabaseConnector::createConnectionDetails(
dbms = "oracle",
user = Sys.getenv("CDM5_ORACLE_USER"),
password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
server = Sys.getenv("CDM5_ORACLE_SERVER"),
port = 1521,
pathToDriver = jdbcDriverFolder
),
cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
workDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
vocabularyDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
cohortTable = "cohort",
tempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA")
)
}

# RedShift
if (!(Sys.getenv("CDM5_REDSHIFT_USER") == ""
& Sys.getenv("CDM5_REDSHIFT_PASSWORD") == ""
& Sys.getenv("CDM5_REDSHIFT_SERVER") == ""
& Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == ""
& Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")) {
DatabaseConnector::downloadJdbcDrivers("redshift")
connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
connectionDetails = DatabaseConnector::createConnectionDetails(
dbms = "redshift",
user = Sys.getenv("CDM5_REDSHIFT_USER"),
password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
server = Sys.getenv("CDM5_REDSHIFT_SERVER"),
port = 5439,
pathToDriver = jdbcDriverFolder
),
cdmDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
cohortTable = "cohort",
tempEmulationSchema = NULL
)
}

# SQL Server
if (!(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") == "")) {
DatabaseConnector::downloadJdbcDrivers("sql server")
connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
connectionDetails = DatabaseConnector::createConnectionDetails(
dbms = "sql server",
user = Sys.getenv("CDM5_SQL_SERVER_USER"),
password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
port = 1433,
pathToDriver = jdbcDriverFolder
),
cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
cohortTable = "cohort",
tempEmulationSchema = NULL
)
}

# Keyring helpers --------------
# Set the keyring name & password for testing
Expand Down

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