tests/testthat/test-translations.R

In dgrapov/CTSgetR: R interface to the Chemical Translation System (CTS) API https://cts.fiehnlab.ucdavis.edu/

#skip_on_cran(tests
context("CTS translation")

#test agains local db or set to NULL to test API
db_name<-'../../inst/ctsgetr.sqlite' # local DB
# init_db<-"test.sqlite"
# tryCatch(unlink(init_db))

#in
id <-
  c(
    "C15973",
    "C00026",
    "C05381",
    "C15972",
    "C00091",
    "C00042",
    "C05379",
    "C00311",
    "C00036",
    "C00024",
    "C00149",
    "C00417",
    "C00158",
    "C00022",
    "C05125",
    "C16254",
    "C00122",
    "C16255",
    "C00074"
  )
from <- "KEGG"
to <- "PubChem CID"

#expected result
res <- structure(list(
  id = c(
    "C15973",
    "C00026",
    "C05381",
    "C15972",
    "C00091",
    "C00042",
    "C05379",
    "C00311",
    "C00036",
    "C00024",
    "C00149",
    "C00417",
    "C00158",
    "C00022",
    "C05125",
    "C16254",
    "C00122",
    "C16255",
    "C00074"
  ),
  `PubChem CID` = c(
    NA,
    "51",
    "440649",
    NA,
    "92133",
    "1110",
    "972",
    "1198",
    "970",
    "444493",
    "222656",
    "643757",
    "19782904",
    "1060",
    "440568",
    NA,
    "21883788",
    NA,
    "1005"
  )
),
class = "data.frame",
row.names = c(NA,-19L))

test_that("one to one translation", {
  skip_on_cran()
  x<-CTSgetR(id, from, to,db_name)
  expect_equivalent(x, res)
  # expect_equal(getwd(), 'foo')
})