tests/manual/test-dbms.R

In IncidencePrevalence: Estimate Incidence and Prevalence using the OMOP Common Data Model

test_that("postgres test", {
  skip_on_cran()
  skip_if(Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "")

  db <- DBI::dbConnect(RPostgres::Postgres(),
    dbname = Sys.getenv("CDM5_POSTGRESQL_DBNAME"),
    host = Sys.getenv("CDM5_POSTGRESQL_HOST"),
    user = Sys.getenv("CDM5_POSTGRESQL_USER"),
    password = Sys.getenv("CDM5_POSTGRESQL_PASSWORD")
  )
  cdm <- CDMConnector::cdmFromCon(
    con = db,
    cdmSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
    writeSchema = c(
      schema = Sys.getenv("CDM5_POSTGRESQL_SCRATCH_SCHEMA"),
      prefix = "incp_"
    )
  )


  # add days
  days_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "day"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!days_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_days(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  # add years
  years_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "year"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!years_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_years(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )


  expect_no_error(postgres_timings <- benchmarkIncidencePrevalence(cdm))
  expect_no_error(postgres_timings_participants <- benchmarkIncidencePrevalence(cdm))

  omopgenerics::cdmDisconnect(cdm = cdm)
})

test_that("redshift test", {
  skip_on_cran()
  skip_if(Sys.getenv("CDM5_REDSHIFT_DBNAME") == "")

  db <- DBI::dbConnect(RPostgres::Redshift(),
    dbname   = Sys.getenv("CDM5_REDSHIFT_DBNAME"),
    host     = Sys.getenv("CDM5_REDSHIFT_HOST"),
    port     = Sys.getenv("CDM5_REDSHIFT_PORT"),
    user     = Sys.getenv("CDM5_REDSHIFT_USER"),
    password = Sys.getenv("CDM5_REDSHIFT_PASSWORD")
  )
  cdm <- CDMConnector::cdmFromCon(
    con = db,
    cdmSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
    writeSchema = c(
      schema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA"),
      prefix = "incp_"
    )
  )


  # add days
  days_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "day"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!days_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_days(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  # add years
  years_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "year"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!years_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_years(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  expect_no_error(redshift_timings <- benchmarkIncidencePrevalence(cdm))
  expect_no_error(redshift_timings_participants <- benchmarkIncidencePrevalence(cdm,
    returnParticipants = TRUE
  ))

  omopgenerics::cdmDisconnect(cdm = cdm)
})

test_that("sql server test", {
  skip_on_cran()
  skip_if(Sys.getenv("CDM5_SQL_SERVER_SERVER") == "")

  db <- DBI::dbConnect(odbc::odbc(),
    Driver = Sys.getenv("SQL_SERVER_DRIVER"),
    Server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
    Database = Sys.getenv("CDM5_SQL_SERVER_CDM_DATABASE"),
    UID = Sys.getenv("CDM5_SQL_SERVER_USER"),
    PWD = Sys.getenv("CDM5_SQL_SERVER_PASSWORD"),
    TrustServerCertificate = "yes",
    Port = Sys.getenv("CDM5_SQL_SERVER_PORT")
  )

  cdm <- CDMConnector::cdmFromCon(
    con = db,
    cdmSchema = strsplit(Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"), "\\.")[[1]],
    writeSchema = c(
      schema = strsplit(Sys.getenv("CDM5_SQL_SERVER_SCRATCH_SCHEMA"), "\\.")[[1]],
      prefix = "incp_"
    )
  )

  # add days
  days_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "day"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!days_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_days(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  # add years
  years_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "year"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!years_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_years(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  expect_no_error(sql_server_timings <- benchmarkIncidencePrevalence(cdm))
  expect_no_error(sql_server_timings_participants <- benchmarkIncidencePrevalence(cdm,
    returnParticipants = TRUE
  ))

  omopgenerics::cdmDisconnect(cdm = cdm)
})

test_that("snowflake test", {
  skip_on_cran()
  skip_if(Sys.getenv("SNOWFLAKE_SERVER") == "")

  con <- DBI::dbConnect(odbc::odbc(),
    SERVER = Sys.getenv("SNOWFLAKE_SERVER"),
    UID = Sys.getenv("SNOWFLAKE_USER"),
    PWD = Sys.getenv("SNOWFLAKE_PASSWORD"),
    DATABASE = Sys.getenv("SNOWFLAKE_DATABASE"),
    WAREHOUSE = Sys.getenv("SNOWFLAKE_WAREHOUSE"),
    DRIVER = Sys.getenv("SNOWFLAKE_DRIVER")
  )

  cdm_schema <- strsplit(Sys.getenv("SNOWFLAKE_CDM_SCHEMA"), "\\.")[[1]]
  write_schema <- strsplit(Sys.getenv("SNOWFLAKE_SCRATCH_SCHEMA"), "\\.")[[1]]

  cdm <- CDMConnector::cdmFromCon(
    con = con,
    cdmSchema = cdm_schema,
    writeSchema = write_schema,
    cdmName = "snowflake"
  )

  # add days
  days_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "day"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!days_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_days(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )

  # add years
  years_q <- addDaysQuery(cdm,
    variable = "observation_period_start_date",
    number = c(1, 2),
    name_style = "a1_{number}",
    type = "year"
  )

  expect_equal(
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::mutate(!!!years_q) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1"),
    cdm$observation_period |>
      utils::head(5) |>
      dplyr::collect() |>
      dplyr::mutate(a1_1 = observation_period_start_date %>% clock::add_years(1)) |>
      dplyr::mutate(a1_1 = as.Date(a1_1)) |>
      dplyr::collect() |>
      dplyr::pull("a1_1")
  )


  expect_no_error(snowflake_timings <- benchmarkIncidencePrevalence(cdm))
  expect_no_error(snowflake_timings_participants <- benchmarkIncidencePrevalence(cdm,
    returnParticipants = TRUE
  ))

  omopgenerics::cdmDisconnect(cdm = cdm)
})