tests/testthat/test_scraper.R

In cdiener/dycone: dycone - analyze the dynamic landscape of metabolome data

# test_scraper.R Copyright 2015 Christian Diener <ch.diener@gmail.com> MIT
# license. See LICENSE for more information.

context("Web scraping")

test_that("HMDB scraping works", {
    ids <- find_hmdb("pyruvate")
    capture.output(concs <- hmdb_concentration(ids[1]))
    expect_true("Pyruvic acid" %in% concs$hmdb_name)
    expect_true(nrow(concs) > 1)
    print(concs)
    expect_true(priority_mean(concs) > 0)
    expect_true(is.na(grep_id("a", "bcd")))
    expect_equal(grep_id("a, b", c("bcd", "ak")), c(a = 2, b = 1))
})

test_that("patching works", {
    miss <- data.frame(id = 1:3, n1 = NA, n2 = c(4, NA, 6), d1 = NA,
                       d2 = c(8, NA, 10))
    ref <- data.frame(id = 2, x = 9)
    aim <- data.frame(id = 1:3, n1 = c(4, 9, 6), n2 = c(4, 9, 6),
                      d1 = 8:10, d2 = 8:10)
    full <- patch(miss, id = 1, 2:3, 4:5, ref_data = ref)
    expect_true(all(aim == full))
})