tests/testthat/test-get_compounds.R

In PubChemR: Interface to the 'PubChem' Database for Chemical Data Retrieval

# compounds <- get_compounds(identifier = c("2244", "1234"),
#                            namespace = "cid")
# testRequest(compounds)
#
# test_that("pulling compounds via an unknown 'namespace'", {
#   tmp <- get_compounds(identifier = c("2244", "1234"),
#                        namespace = "taxonomy")
#   expect_false(allSuccess(tmp))
# })
#
# test_that("get_compounds() returns an object of class 'PubChemInstanceList'",
#           {
#             expect_true("PubChemInstanceList" %in% class(compounds))
#           })
#
# # test for 'namespace' arg. ----
# tmp <- get_compounds(identifier = "aspirin",
#                      namespace = "name")
# testRequest(tmp)
#
# tmp <- get_compounds(identifier = "CC(=O)OC1=CC=CC=C1C(=O)O",
#                      namespace = "smiles")
# testRequest(tmp)
#
# test_that("handling undefined/unknown/incorrect compounds. returns error.",
#           {
#             tmp <- get_compounds(identifier = -1,
#                                  namespace = "cid")
#
#             expect_false(tmp$result[[1]]$success)
#             expect_true(!is.null(tmp$result[[1]]$error))
#           })
#
# # instance() tests. ----
# test_that("instance() returns an object of class 'PubChemInstance'", {
#   expect_true("PubChemInstance" %in% class(instance(compounds)))
#   expect_output(print(instance(compounds)), "An object of class 'PubChemInstance'")
# })
#
# # retrieve() tests ----
# test_that("retrieve() returns selected slots as expected for a compound", {
#   expect_identical(
#     retrieve(
#       compounds,
#       .slot = "id",
#       .which = "2244",
#       .to.data.frame = TRUE
#     ),
#     retrieve(
#       instance(compounds, "2244"),
#       .slot = "id",
#       .to.data.frame = TRUE
#     )
#   )
#
#   expect_identical(
#     retrieve(
#       compounds,
#       .slot = "id",
#       .which = "2244",
#       .to.data.frame = FALSE
#     ),
#     retrieve(
#       instance(compounds, "2244"),
#       .slot = "id",
#       .to.data.frame = FALSE
#     )
#   )
#
#   # Return results invisibly when .verbose = TRUE
#   expect_invisible(
#     retrieve(
#       compounds,
#       .slot = "id",
#       .to.data.frame = FALSE,
#       .combine.all = TRUE,
#       .verbose = TRUE
#     )
#   )
#
#   # Combine all compounds into a data.frame
#   expect_true({
#     tmp <-
#       retrieve(
#         compounds,
#         .slot = "atoms",
#         .to.data.frame = TRUE,
#         .combine.all = TRUE,
#         .verbose = FALSE
#       )
#     all(request_args(compounds, "identifier") %in% tmp[["Identifier"]])
#   })
# })
#
# test_that("retrieve() returns error when unknown/undefined slots or identifiers are provided.",
#           {
#             expect_error(retrieve(compounds, .which = "dncr"))
#             expect_warning(retrieve(compounds, .which = "1234"))
#             expect_true({
#               tmp <- suppressWarnings(retrieve(compounds, .which = "1234"))
#               is.null(tmp)
#             })
#
#             expect_null(retrieve(compounds, .which = "1234", .slot = "unkown_slot"))
#           })
#
# test_that("checking the effect of '.verbose' argument in retrieve() function",
#           {
#             expect_invisible(retrieve(
#               compounds,
#               .slot = "id",
#               .verbose = TRUE,
#               .combine.all = TRUE
#             ))
#           })