tests/testthat/test_annotation.R

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

# test_that("AnnotationParams", {
#     expect_error(setAnnotationParams(1),
#                  "'params' must be of class 'AnnotationParams'.")
#     expect_error(setAnnotationParams(inputs = 1),
#                  "'inputs' must contain a species and a feature type.")
#     expect_error(setAnnotationParams(inputs = LETTERS[1:2]),
#                  "Couldn't find a unique species match for 'A'.")
#     expect_error(setAnnotationParams(inputs = c("Human genes", "foo")),
#                  "Couldn't find a unique feature type match for 'foo'.")
# 
#     ap <- setAnnotationParams(inputs = c("Human genes",
#                                          "UniProtKB/Swiss-Prot ID"))
#     expect_null(show(ap))
# 
#     expect_is(ap, "AnnotationParams")
#     expect_identical(ap@martname, "ENSEMBL_MART_ENSEMBL")
#     expect_identical(ap@dataset, "hsapiens_gene_ensembl")
#     expect_identical(ap@filter, "uniprotswissprot")
#     expect_error(setAnnotationParams()) ## only in non-interactive mode
# 
#     ap2 <- getAnnotationParams()
#     expect_identical(ap, ap2)
#     setAnnotationParams(ap)
#     ap2 <- getAnnotationParams()
#     expect_identical(ap, ap2)
# })