tests/testthat/test-datasets-sparse.R

In FASTGenomics/r_client: Manage FASTGenomics Instances

context("test-datasets-sparse")
library(Matrix)

gen_data <- function() {
  cell_metadata = data.frame(cellId = c("cell_1", "cell_2", "cell_3"))
  gene_metadata = data.frame(geneId = c("gene_1", "gene_2", "gene_3"))
  matrix = sparseMatrix(
    i = c(1, 2),
    j = c(2, 3),
    x = c(4, 5),
    giveCsparse = FALSE,
    dims = c(3, 3),
    dimnames = list(gene_metadata$geneId, cell_metadata$cellId)
  )
  return(list(
    cells = cell_metadata,
    genes = gene_metadata,
    matrix = matrix
  ))
}

gen_args <- function(replacements = list()) {
  BEARER_PAT = Sys.getenv("FG_PAT")
  BEARER_EMAIL = Sys.getenv("FG_EMAIL")
  BASE_URL = Sys.getenv("FGBASEURL")
  default_conn <-
    FGConnection$new(base_url = BASE_URL,
                     pat = BEARER_PAT,
                     email = BEARER_EMAIL)
  input = gen_data()
  dir.create("./temp", showWarnings = FALSE)
  tmpdir = file.path("./temp",
                     stringi::stri_rand_strings(n = 1, length = 20)[[1]])
  args = list(
    connection = default_conn,
    matrix = input$matrix,
    cell_metadata = input$cells,
    gene_metadata = input$genes,
    title = "R client test",
    description = "description",
    organism_id = 9606,
    gene_nomenclature = "GeneSymbol",
    tmpdir = tmpdir,
    zipfiles = TRUE
  )
  args[names(replacements)] = replacements
  args
}

test_that("create-sparse: can create a dataset, unzipped", {
  args <- gen_args(list(zipfiles = FALSE))
  result <- do.call(create_dataset_df, args)
  expect_is(result, "FGResponse")
})

test_that("create-sparse: can create a dataset, zipped", {
  args <- gen_args(list(zipfiles = TRUE))
  result <- do.call(create_dataset_df, args)
  expect_is(result, "FGResponse")
})

test_that("create-sparse: can create a dataset, dgCMatrix", {
  args <- gen_args(list(matrix = as(gen_data()$matrix, "dgCMatrix")))
  result <- do.call(create_dataset_df, args)
  expect_is(result, "FGResponse")
})

test_that("create-sparse: does not change working directory", {
  args <- gen_args()
  result <- do.call(create_dataset_df, args)
  oldwd <- getwd()
  expect_true(getwd() == oldwd)
})

test_that("create-sparse: temp directory is empty after the submission", {
  args <- gen_args()
  result <- do.call(create_dataset_df, args)
  expect_true(length(list.files(args$tmpdir)) == 0)
})

test_that("create-sparse: can poll upload status", {
  args <- gen_args()
  result <- do.call(create_dataset_df, args)
  status <-
    poll_dataset_until_validated(args$connection, result)
  expect_true(status)
})

test_that("create-sparse: wrong matrix type", {
  args <- gen_args(list(matrix = "abc"))
  expect_error(
    do.call(create_dataset_df, args),
    "Unsupported matrix format, expected a \"sparseMatrix\"."
  )
})

test_that("create-sparse: wrong cell_metadata type", {
  args <- gen_args(list(cell_metadata = "abc"))
  expect_error(do.call(create_dataset_df, args),
               "cell_metadata must be a data frame.")
})

test_that("create-sparse: wrong gene_metadata type", {
  args <- gen_args(list(gene_metadata = "abc"))
  expect_error(do.call(create_dataset_df, args),
               "gene_metadata must be a data frame.")
})

test_that("create-sparse: cell_metadata has no cellId", {
  args <- gen_args(list(cell_metadata = data.frame()))
  expect_error(do.call(create_dataset_df, args),
               "cell_metadata must have a cellId column.")
})

test_that("create-sparse: gene_metadata has no geneId", {
  args <- gen_args(list(gene_metadata = data.frame()))
  expect_error(do.call(create_dataset_df, args),
               "gene_metadata must have a geneId column.")
})

test_that("create-sparse: no common cell names", {
  args <- gen_args(list(cell_metadata = data.frame(cellId = c(1, 2, 3))))
  expect_error(
    do.call(create_dataset_df, args),
    "No common cell names found in matrix and cell_metadata."
  )
})

test_that("create-sparse: no common gene names", {
  args <- gen_args(list(gene_metadata = data.frame(geneId = c(1, 2, 3))))
  expect_error(
    do.call(create_dataset_df, args),
    "No common gene names found in matrix and gene_metadata."
  )
})

test_that("create-sparse: title too short", {
  args <- gen_args(list(title = "a"))
  expect_error(
    do.call(create_dataset_df, args),
    "Title has to be a string with length between 5 and 200."
  )
})