tests/testthat/test-classification.R

In bakaburg1/BaySREn: BaySREn. An R package to automatise citation collection and screening in Systematic Reviews. Based on Bayesian active machine learning

oldMem <- getOption("baysren.BartMem")

withr::defer(
  {
    options(baysren.BartMem = oldMem)
    unlink(list.files(pattern = ".pID", all.files = TRUE))
    unlink("Model_backup.rds")
    unlink("Sessions/Session1/Annotations/", recursive = TRUE)
    unlink("Sessions/Session1/Results/", recursive = TRUE)
    unlink("Sessions/Session1/Samples/", recursive = TRUE)
    unlink("Sessions/Session1/DTM.rds", recursive = TRUE)
  },
  teardown_env()
)

options(baysren.BartMem = "16")

test_that("annotation file classification doesn't throw errors.", {
  set.seed(1482398429)

  expect_error(enrich_annotation_file("Session1", pos_mult = 20, n_models = 2, autorun = TRUE, limits = list(
    stop_after = 2, pos_target = NULL,
    labeling_limit = NULL
  )), NA)
})

session_files <- get_session_files("Session1", sessions_folder = "Sessions")

sessions_files_exist <- test_that("the expected number of files was created.", {
  exp <- c(Records = 1L, Annotations = 3L, DTM = 1L, Samples = 3L, Results = 3L)

  obs <- session_files %>% sapply(length)

  expect_mapequal(obs, exp)
})

# TODO: renable once reproducible predictions are implemented
# if (isTRUE(sessions_files_exist)) {
#   test_that("DTM matches expectation.", {
#     expect_snapshot_file(session_files$DTM)
#   })
#
#   #  There should be three versions of each file type, so no dynamic init here
#   for (i in 1:3) {
#     test_that(paste("Samples file", i, "matches expectation."), {
#       data <- import_data(session_files$Samples[i])[1:20, 1:20] # Limit memory footprint
#       expect_snapshot_value(data, style = "serialize")
#     })
#
#     test_that(paste("Record file", i, "matches expectation."), {
#       data <- import_data(session_files$Results[i])[-2, ] # Remove fields with timestamps
#       expect_snapshot_value(data, style = "deparse")
#     })
#
#     test_that(paste("Annotation file", i, "matches expectation."), {
#       data <- import_data(session_files$Annotations[i]) %>%
#         select(matches("^(Prev_|Rev_|Order)")) %>% # Keep varying fields
#         head(20)
#       expect_snapshot_value(data, style = "serialize")
#     })
#   }
# }