tests/testthat/test_metadata.R

In bioturing/rBCS: Handle BioTuring Compressed File

test_that("Read normal metadata", {
  meta.dir <- tempdir()
  info <- list(
    id = "test",
    name = "test metadata",
    clusters = c(0, 0, 1),
    clusterName = c("Unassigned", "A"),
    clusterLength = c(2, 1),
    type = "category",
    history = list(CreateCommit())
  )
  jsonlite::write_json(info, file.path(meta.dir, "test.json"), auto_unbox=TRUE)
  jsonlite::write_json(list(
    content = list(test = info),
    version = 1,
    default = 'test'
  ), file.path(meta.dir, "metalist.json"), auto_unbox=TRUE)

  meta <- Metadata$new(meta.dir, JSONFile)
  data <- meta$get("test")
  expect_equal(length(data), 3)
  expect_equal(length(levels(data)), 2)
})

test_that("Read old metadata", {
  meta.dir <- tempdir()
  info <- list(
    id = "test",
    name = "test metadata",
    clusters = c(0, 0, 1),
    clusterName = c("Unassigned", "A"),
    clusterLength = c(2, 1),
    type = "category",
    history = list(CreateCommit())
  )
  jsonlite::write_json(info, file.path(meta.dir, "test.json"), auto_unbox=TRUE)
  jsonlite::write_json(list(test = info), file.path(meta.dir, "metalist.json"), auto_unbox=TRUE)

  meta <- Metadata$new(meta.dir, JSONFile)
  data <- meta$get("test")
  expect_equal(length(data), 3)
  expect_equal(length(levels(data)), 2)
})

test_that("Read data no type", {
  meta.dir <- tempdir()
  info <- list(
    id = "test",
    name = "test metadata",
    clusters = c(0, 0, 1),
    clusterName = c("Unassigned", "A"),
    clusterLength = c(2, 1),
    history = list(CreateCommit())
  )
  jsonlite::write_json(info, file.path(meta.dir, "test.json"), auto_unbox=TRUE)
  jsonlite::write_json(list(
    content = list(test = info),
    version = 1,
    default = 'test'
  ), file.path(meta.dir, "metalist.json"), auto_unbox=TRUE)

  meta <- Metadata$new(meta.dir, JSONFile)
  data <- meta$get("test")
  expect_equal(length(data), 3)
  expect_equal(length(levels(data)), 2)
})

test_that("Read data no id", {
  meta.dir <- tempdir()
  info <- list(
    name = "test metadata",
    clusters = c(0, 0, 1),
    clusterName = c("Unassigned", "A"),
    clusterLength = c(2, 1),
    history = list(CreateCommit())
  )
  jsonlite::write_json(info, file.path(meta.dir, "test.json"), auto_unbox=TRUE)
  jsonlite::write_json(list(
    content = list(test = info),
    version = 1,
    default = 'test'
  ), file.path(meta.dir, "metalist.json"), auto_unbox=TRUE)

  meta <- Metadata$new(meta.dir, JSONFile)
  data <- meta$get("test")
  expect_equal(length(data), 3)
  expect_equal(length(levels(data)), 2)
})

test_that("Read data no info", {
  meta.dir <- tempdir()
  info <- list(
    name = "test metadata",
    clusters = c(0, 0, 1),
    clusterName = c("Unassigned", "A"),
    clusterLength = c(2, 1),
    history = list(CreateCommit())
  )
  jsonlite::write_json(info$clusters, file.path(meta.dir, "test.json"), auto_unbox=TRUE)
  jsonlite::write_json(list(test = info), file.path(meta.dir, "metalist.json"), auto_unbox=TRUE)

  meta <- Metadata$new(meta.dir, JSONFile)
  data <- meta$get("test")
  expect_equal(length(data), 3)
  expect_equal(length(levels(data)), 2)
})

test_that("Duplicates in metadata", {
  meta.dir <- tempdir()
  metalist <- file.path(meta.dir, "metalist.json")
  if (file.exists(metalist)) file.remove(metalist)
  meta <- Metadata$new(meta.dir, JSONFile)
  id <- meta$add(c("a", "Unassigned ", NA), "test")
  data.r <- meta$get(id)
  expect_equal(length(levels(data.r)), 2)
})