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Putting all unit tests in a loop
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Schuemie authored and Schuemie committed Oct 21, 2023
1 parent 2b6e31c commit faa68ea
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128 changes: 8 additions & 120 deletions tests/testthat/test-dataHash.R
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@@ -1,122 +1,10 @@
library(testthat)

test_that("Compute data hash", {
# Postgresql -----------------------------------------------------------------
details <- createConnectionDetails(
dbms = "postgresql",
user = Sys.getenv("CDM5_POSTGRESQL_USER"),
password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
server = Sys.getenv("CDM5_POSTGRESQL_SERVER")
)
connection <- connect(details)
hash <- computeDataHash(connection, Sys.getenv("CDM5_POSTGRESQL_CDM54_SCHEMA"))
expect_true(is.character(hash))

disconnect(connection)

# 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")
)
connection <- connect(details)
hash <- computeDataHash(connection, Sys.getenv("CDM5_SQL_SERVER_CDM54_SCHEMA"))
expect_true(is.character(hash))

disconnect(connection)

# Oracle ---------------------------------------------------------------------
details <- createConnectionDetails(
dbms = "oracle",
user = Sys.getenv("CDM5_ORACLE_USER"),
password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
server = Sys.getenv("CDM5_ORACLE_SERVER")
)
connection <- connect(details)
hash <- computeDataHash(connection, Sys.getenv("CDM5_ORACLE_CDM54_SCHEMA"))
expect_true(is.character(hash))

disconnect(connection)

# RedShift ------------------------------------------------------------------
details <- createConnectionDetails(
dbms = "redshift",
user = Sys.getenv("CDM5_REDSHIFT_USER"),
password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
server = Sys.getenv("CDM5_REDSHIFT_SERVER")
)
connection <- connect(details)
hash <- computeDataHash(connection, Sys.getenv("CDM5_REDSHIFT_CDM54_SCHEMA"))
expect_true(is.character(hash))

disconnect(connection)

# RSQLite --------------------------------------------------------------------
dbFile <- tempfile(fileext = "sqlite")
details <- createConnectionDetails(
dbms = "sqlite",
server = dbFile
)
connection <- connect(details)
DatabaseConnector::insertTable(
connection = connection,
databaseSchema = "main",
tableName = "cars",
data = cars,
createTable = TRUE
)
DatabaseConnector::insertTable(
connection = connection,
databaseSchema = "main",
tableName = "iris",
data = iris,
createTable = TRUE
)
hash <- computeDataHash(connection, "main")
expect_true(is.character(hash))

disconnect(connection)
unlink(dbFile)

# DuckDB --------------------------------------------------------------------
dbFile <- tempfile(fileext = "duckdb")
details <- createConnectionDetails(
dbms = "duckdb",
server = dbFile
)
connection <- connect(details)
DatabaseConnector::insertTable(
connection = connection,
databaseSchema = "main",
tableName = "cars",
data = cars,
createTable = TRUE
)
DatabaseConnector::insertTable(
connection = connection,
databaseSchema = "main",
tableName = "iris",
data = iris,
createTable = TRUE
)
hash <- computeDataHash(connection, "main")
expect_true(is.character(hash))

disconnect(connection)
unlink(dbFile)

# Snowflake ------------------------------------------------------------------
details <- createConnectionDetails(
dbms = "snowflake",
user = Sys.getenv("CDM_SNOWFLAKE_USER"),
password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
)
connection <- connect(details)
hash <- computeDataHash(connection, Sys.getenv("CDM_SNOWFLAKE_CDM53_SCHEMA"))
expect_true(is.character(hash))

disconnect(connection)
})
for (testServer in testServers) {
test_that(addDbmsToLabel("Compute data hash", testServer), {
connection <- connect(testServer$connectionDetails)
on.exit(disconnect(connection))
hash <- computeDataHash(connection, testServer$cdmDatabaseSchema)
expect_true(is.character(hash))
})
}
142 changes: 11 additions & 131 deletions tests/testthat/test-dbplyr.R
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Expand Up @@ -2,148 +2,28 @@ library(testthat)
library(DatabaseConnector)
source("dbplyrTestFunction.R")

test_that("Test dbplyr on Postgres", {
# Postgres ----------------------------------------------------------
connectionDetails <- createConnectionDetails(
dbms = "postgresql",
user = Sys.getenv("CDM5_POSTGRESQL_USER"),
password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
server = Sys.getenv("CDM5_POSTGRESQL_SERVER")
)
cdmDatabaseSchema <- Sys.getenv("CDM5_POSTGRESQL_CDM54_SCHEMA")
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
})

test_that("Test dbplyr on SQL Server", {
# SQL Server --------------------------------------
connectionDetails <- 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")
)
cdmDatabaseSchema <- Sys.getenv("CDM5_SQL_SERVER_CDM54_SCHEMA")
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
})

test_that("Test dbplyr on Oracle", {
# Oracle ---------------------------------------
connectionDetails <- createConnectionDetails(
dbms = "oracle",
user = Sys.getenv("CDM5_ORACLE_USER"),
password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
server = Sys.getenv("CDM5_ORACLE_SERVER")
)
cdmDatabaseSchema <- Sys.getenv("CDM5_ORACLE_CDM54_SCHEMA")
options(sqlRenderTempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"))
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
})

test_that("Test dbplyr on RedShift", {
# RedShift ----------------------------------------------
connectionDetails <- createConnectionDetails(
dbms = "redshift",
user = Sys.getenv("CDM5_REDSHIFT_USER"),
password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
server = Sys.getenv("CDM5_REDSHIFT_SERVER")
)
cdmDatabaseSchema <- Sys.getenv("CDM5_REDSHIFT_CDM54_SCHEMA")
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
})

test_that("Test dbplyr on SQLite", {
# SQLite -------------------------------------------------
databaseFile <- tempfile(fileext = ".sqlite")
cdmDatabaseSchema <- "main"
connectionDetails <- createConnectionDetails(
dbms = "sqlite",
server = databaseFile
)
connection <- connect(connectionDetails)
insertTable(
connection = connection,
databaseSchema = cdmDatabaseSchema,
tableName = "person",
data = data.frame(person_id = seq_len(100),
year_of_birth = round(runif(100, 1900, 2000)),
race_concept_id = as.numeric(NA),
gender_concept_id = rep(c(8507, 8532), 50),
care_site_id = round(runif(100, 1, 1e7)))
)
insertTable(
connection = connection,
databaseSchema = cdmDatabaseSchema,
tableName = "observation_period",
data = data.frame(person_id = seq_len(100),
observation_period_start_date = rep(as.Date("2000-01-01"), 100),
observation_period_end_date = rep(as.Date(c("2000-06-01", "2001-12-31")), 50),
period_type_concept_id = rep(0, 100))
)
disconnect(connection)
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
unlink(databaseFile)
})

test_that("Test dbplyr on DuckDB", {
# DuckDb -------------------------------------------------
databaseFile <- tempfile(fileext = ".duckdb")
cdmDatabaseSchema <- "main"
connectionDetails <- createConnectionDetails(
dbms = "duckdb",
server = databaseFile
)
connection <- connect(connectionDetails)
insertTable(
connection = connection,
databaseSchema = cdmDatabaseSchema,
tableName = "person",
data = data.frame(person_id = seq_len(100),
year_of_birth = round(runif(100, 1900, 2000)),
race_concept_id = as.numeric(NA),
gender_concept_id = rep(c(8507, 8532), 50),
care_site_id = round(runif(100, 1, 1e7)))
)
insertTable(
connection = connection,
databaseSchema = cdmDatabaseSchema,
tableName = "observation_period",
data = data.frame(person_id = seq_len(100),
observation_period_start_date = rep(as.Date("2000-01-01"), 100),
observation_period_end_date = rep(as.Date(c("2000-06-01", "2001-12-31")), 50),
period_type_concept_id = rep(0, 100))
)
disconnect(connection)
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
unlink(databaseFile)
})

test_that("Test dbplyr on Snowflake", {
# Snowflake ----------------------------------------------
connectionDetails <- createConnectionDetails(
dbms = "snowflake",
user = Sys.getenv("CDM_SNOWFLAKE_USER"),
password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
)
cdmDatabaseSchema <- Sys.getenv("CDM_SNOWFLAKE_CDM53_SCHEMA")
options(sqlRenderTempEmulationSchema = Sys.getenv("CDM_SNOWFLAKE_OHDSI_SCHEMA"))
testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
})
for (testServer in testServers) {
test_that(addDbmsToLabel("Test dbplyr", testServer), {
options(sqlRenderTempEmulationSchema = testServer$tempEmulationSchema)
testDbplyrFunctions(connectionDetails = testServer$connectionDetails,
cdmDatabaseSchema = testServer$cdmDatabaseSchema)
})
}

test_that("Test dbplyr date functions on non-dbplyr data", {
date <- c(as.Date("2000-02-01"), as.Date("2000-12-31"), as.Date("2000-01-31"))

date2 <- c(as.Date("2000-02-05"), as.Date("2000-11-30"), as.Date("2002-01-31"))

expect_equal(dateDiff("day", date, date2), c(4, -31, 731))

expect_equal(eoMonth(date), c(as.Date("2000-02-29"), as.Date("2000-12-31"), as.Date("2000-01-31")))

expect_equal(dateAdd("day", 1, date), c(as.Date("2000-02-02"), as.Date("2001-01-01"), as.Date("2000-02-01")))

expect_equal(year(date), c(2000, 2000, 2000))

expect_equal(month(date), c(2, 12, 1))

expect_equal(day(date), c(1, 31, 31))
})
67 changes: 0 additions & 67 deletions tests/testthat/test-duckdb.R
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