tests/testthat/test-mw.R

In lipidr: Data Mining and Analysis of Lipidomics Datasets

library(lipidr)
context("test-mw")
test_that("can list studies for a specific keyword", {
  skip_on_bioc()
  skip_if_offline("www.metabolomicsworkbench.org")
  res <- list_mw_studies(keyword = "lipidomics")
  expect_gt(nrow(res), 30)
  expect_equal(ncol(res), 9)
  na_cols <- sapply(res, function(x) all(is.na(x)))
  expect_false(any(na_cols))
})
test_that("can fetch study by id", {
  skip_on_bioc()
  skip_if_offline("www.metabolomicsworkbench.org")
  expect_warning(
    res <- fetch_mw_study("ST001111"),
    "Some lipid names couldn't be parsed"
  )
  expect_valid_lipidex(res, c(777, 118))
  row_data <- rowData(res)
  expect_equal(unique(row_data$filename), c("AN001805", "AN001806"))
  expect_lt(sum(row_data$not_matched), 10)
})

test_that("can fetch study with sample names", {
  skip_on_bioc()
  skip_if_offline("www.metabolomicsworkbench.org")
  res <- fetch_mw_study("ST001323")
  expect_valid_lipidex(res, c(277, 58))
  row_data <- rowData(res)
  expect_equal(unique(row_data$filename), c("AN002199", "AN002200", "AN002201"))
  expect_equal(sum(row_data$not_matched), 1)
  col_data <- colData(res)
  expect_equal(colnames(col_data), c("BileAcid", "Diet", "RAW_FILE_NAME"))
})