tests/testthat/test-check-genie-access.R

In genieBPC: Project GENIE BioPharma Collaborative Data Processing Pipeline

# Full Access PAT ---------------------------------------------------------

test_that("Test no error with full access PAT", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT"))
  expect_no_error(check_genie_access(pat = Sys.getenv("SYNAPSE_PAT")))
})

# * Consortium Specific Check ----

test_that("Test no error with full access PAT and consortium check", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT"))
  expect_no_error(
    check_genie_access(pat = Sys.getenv("SYNAPSE_PAT"),
                       check_consortium_access = TRUE))
})

# Public Access PAT ---------------------------------------------------------

test_that("Test no error with Public access PAT, not consortium specific check", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC"))
  expect_no_error(check_genie_access(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC")))
})


# * Consortium Specific Check ---

test_that("Test error with public access PAT and consortium check", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC"))
  expect_error(
    check_genie_access(pat = Sys.getenv("SYNAPSE_PAT_PUBLIC"),
                       check_consortium_access = TRUE))
})

# NO TERMS ---------------------------------------------------------

test_that("Test no error when access but terms not checked", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS"))
  expect_no_error(check_genie_access(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS")))
})

test_that("Test error when pulling PUBLIC data but terms not checked", {
  skip_if_not(.is_connected_to_genie(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS")))

  set_synapse_credentials(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS"))
  expect_no_error(check_genie_access(pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS")))

  expect_error(pull_data_synapse(
    cohort = c("CRC"),
    version = c("v2.0-public"),
    pat = Sys.getenv("SYNAPSE_PAT_NO_TERMS")
  ))

})