tests/testthat/test-metabolomics_data_dictionary.R

In MoTrPAC/MotrpacBicQC: QC/QA functions for the MoTrPAC community

# context("Test metabolomics data dictionary")
# 
# 
# test_that("Metabolomics data dictionary", {
#   # expected_mdd_colnames <- c("CURRENT_REFMET_NAME", "refmet_name", "metabolite_name", "is_standard", "super_class", "main_class", "sub_class", "formula", "exactmass", "pubchem_cid", "kegg_id", "inchi_key", "lm_id", "hmdb_id", "chebi_id")
#   expected_mdd_colnames <- c("refmet_name")
#   mdd <- get_and_validate_mdd()
#   expect_equal( setequal(expected_mdd_colnames, colnames(mdd)), TRUE)
#   expect_gt(dim(mdd)[1], 2000)
#   expect_false(any(duplicated(mdd$refmet_name)))
# })

# test_that("REST service from RefMet works and return right number of columns and values", {
#   expected_mdd_colnames <- c("refmet_name", "super_class", "main_class", "sub_class", "formula", "exactmass", "inchi_key", "pubchem_cid", "kegg_id", "standard")
#   mdd <- get_and_validate_mdd()
#   expect_equal( setequal(expected_mdd_colnames, colnames(mdd)), TRUE)
#   expect_gt(dim(mdd)[1], 2000)
# })

# test_that("Checking that REST service from Refmet works", {
#   good_one <- "citrate"
#   bad_one <- "testfail"
#   expect_equal(validate_refmetname())
# })