longtests/testthat/test-PANTHER.R

In acidgenomics/PANTHER: PANTHER

organisms <- sort(names(.pantherMappings))

## Here's how to obtain supported releases.
## > releases <- setdiff(.pantherReleases, "current_release")

test_that("PANTHER : 11.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 15010L,
            "Drosophila melanogaster" = 10610L,
            "Homo sapiens" = 19753L,
            "Mus musculus" = 21090L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "11.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

test_that("PANTHER : 12.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 14127L,
            "Drosophila melanogaster" = 10030L,
            "Homo sapiens" = 19556L,
            "Mus musculus" = 20884L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "12.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

test_that("PANTHER : 13.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 13494L,
            "Drosophila melanogaster" = 10087L,
            "Homo sapiens" = 18599L,
            "Mus musculus" = 19822L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "13.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

test_that("PANTHER : 13.1", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 13806L,
            "Drosophila melanogaster" = 10349L,
            "Homo sapiens" = 19669L,
            "Mus musculus" = 20930L
        ),
        f = function(organism, nrow) {
            ## NOTE C. elegans file here has parsing issues.
            suppressWarnings({
                object <- PANTHER(organism = organism, release = "13.1")
            })
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

test_that("PANTHER : 14.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 14298L,
            "Drosophila melanogaster" = 10547L,
            "Homo sapiens" = 19767L,
            "Mus musculus" = 21059L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "14.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

## NOTE The 15.0 release is messed up on the FTP server.

test_that("PANTHER : 16.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 14426L,
            "Drosophila melanogaster" = 10656L,
            "Homo sapiens" = 19511L,
            "Mus musculus" = 20986L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "16.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})

test_that("PANTHER : 17.0", {
    Map(
        organism = organisms,
        nrow = c(
            "Caenorhabditis elegans" = 14447L,
            "Drosophila melanogaster" = 11033L,
            "Homo sapiens" = 19343L,
            "Mus musculus" = 20862L
        ),
        f = function(organism, nrow) {
            object <- PANTHER(organism = organism, release = "17.0")
            expect_s4_class(object, "PANTHER")
            expect_identical(nrow(object), nrow)
        }
    )
})