tests/testthat/test_obo.R

In rmzqc: Creation, Reading and Validation of 'mzqc' Files

##
## Author: Chris Bielow
##

test_that("getCVDictionary = function()", {
  ## this should never fail (even if internet is broken)
  cv = getCVDictionary(use_local_fallback = TRUE)
  expect_true(all(c("CV", "URI", "version") %in% names(cv)))
  expect_true(all(c("id", "name", "def") %in% names(cv$CV)))
  expect_true("MS:1001000" %in% cv$CV$id)
  expect_true("gene name" %in% cv$CV$name)

  ## this should never fail, due to local fallback (even if with wrong URL)
  cv = getCVDictionary(source="custom", custom_uri = "https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo", use_local_fallback = TRUE)
  expect_true(all(c("CV", "URI", "version") %in% names(cv)))

  ## this should always fail (due to wrong URL)
  cv = try(getCVDictionary(source="custom", custom_uri = "https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo", use_local_fallback = FALSE))
  expect_true(inherits(cv, "try-error"))
})

test_that("getLatest_PSICV_URL = function()", {
  ## this test requires internet connection - in particular to Github (checking other sites may not help), so run it only if available:
  con = try(url("https://api.github.com", open="r"))
  if (!inherits(con, "try-error")) {
    close(con)
    expect_true(endsWith(getLatest_PSICV_URL(), "psi-ms.obo"))
  }
})

test_that("getLocal_CV_Version = function()", {
  expect_true(getLocal_CV_Version(system.file("./cv/psi-ms.obo", package="rmzqc")) == "4.1.129")
})

test_that("getCVInfo = function()", {
  expect_true(startsWith(getCVInfo()$name, "Proteomics Standards Initi"))
})

test_that("getCVSingleton()", {
  d1 = getCVSingleton()
  d2 = getCVSingleton()
  expect_true(identical(d1$getData(), d2$getData()))
  entry = d1$byID("MS:1000563")
  expect_true(entry$parents == "MS:1000560")
  suppressWarnings(expect_null(d1$byID("does_not_exit")))
})