library(testthat)
# These tests currently just check if the main achilles function and export functiosn don't throw any errors on the different platforms
# Note: Currently only checking CDM v5
test_that("Achilles main does not throw an error on Postgres", {
# Postgresql
details <- createConnectionDetails(dbms = "postgresql",
user = Sys.getenv("CDM5_POSTGRESQL_USER"),
password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
server = Sys.getenv("CDM5_POSTGRESQL_SERVER"))
try(result <- achilles(details,
cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
sourceName = "NHANES",
cdmVersion = "5",
validateSchema = FALSE,
createTable = TRUE))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
expect_true(class(result) == "achillesResults")
})
test_that("Achilles main does not throw an error on SQL Server", {
# SQL Server
details <- createConnectionDetails(dbms = "sql server",
user = Sys.getenv("CDM5_SQL_SERVER_USER"),
password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
server = Sys.getenv("CDM5_SQL_SERVER_SERVER"))
try(result <- achilles(details,
cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
sourceName = "NHANES",
cdmVersion = "5",
validateSchema = FALSE,
createTable = TRUE))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
expect_true(class(result) == "achillesResults")
})
test_that("Achilles main does not throw an error on Oracle", {
# Oracle
details <- createConnectionDetails(dbms = "oracle",
user = Sys.getenv("CDM5_ORACLE_USER"),
password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
server = Sys.getenv("CDM5_ORACLE_SERVER"))
try(result <- achilles(details,
cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
oracleTempSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
sourceName = "NHANES",
cdmVersion = "5",
validateSchema = FALSE,
createTable = TRUE))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
expect_true(class(result) == "achillesResults")
})
test_that("Achilles export does not throw an error on Postgres", {
# Postgresql
details <- createConnectionDetails(dbms = "postgresql",
user = Sys.getenv("CDM5_POSTGRESQL_USER"),
password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
server = Sys.getenv("CDM5_POSTGRESQL_SERVER"))
try(exportToJson(details,
cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
outputPath = "postgresql",
cdmVersion = "5"))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
# dashboard.json is the last report to be generated:
expect_true(file.exists("postgresql/dashboard.json"))
})
test_that("Achilles export does not throw an error on SQL Server", {
# SQL Server
details <- 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"))
try(exportToJson(details,
cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
outputPath = "sql_server",
cdmVersion = "5"))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
# dashboard.json is the last report to be generated:
expect_true(file.exists("sql_server/dashboard.json"))
})
test_that("Achilles export does not throw an error on Oracle", {
# Oracle
details <- createConnectionDetails(dbms = "oracle",
user = Sys.getenv("CDM5_ORACLE_USER"),
password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
server = Sys.getenv("CDM5_ORACLE_SERVER"))
try(exportToJson(details,
cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
resultsDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
outputPath = "oracle",
cdmVersion = "5"))
if (file.exists("errorReport.txt")){
writeLines(readChar("errorReport.txt", file.info("errorReport.txt")$size))
}
# dashboard.json is the last report to be generated:
expect_true(file.exists("oracle/dashboard.json"))
})
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