tests/testthat/test-annotate_with_ncbi.r

In currocam/utilsHMMER: HMMERutils

skip_if_not_installed("taxizedb")

test_that("Danio rerio sequential, length one, offline", {
    df <- annotate_with_NCBI_taxid(7955, "species", mode = "local")
    expect_identical(df$species[[1]], "Danio rerio")
})

test_that(
    "Danio rerio & Phascolarctos cinereus sequential, length 2, offline",
    {
        df <- annotate_with_NCBI_taxid(
            c(7955, 38626), c("species", "phylum"),
            mode = "local"
        )
        check <- c("Danio rerio", "Phascolarctos cinereus")
        df %>%
            dplyr::pull(species) %>%
            expect_setequal(check)
    }
)

test_that("Danio rerio sequential all, offline", {
    annotate_with_NCBI_taxid(7955, mode = "local") %>%
        testthat::expect_error(NA)
})

testthat::skip("No mocking for add fullseqfasta yet")
skip_if_not_installed("taxize")
test_that("Danio rerio sequential, length one, online", {
    df <- annotate_with_NCBI_taxid(7955, "species")
    df_check <- tibble::tibble(species = "Danio rerio", taxid = "7955")
    expect_identical(df, df_check)
})

test_that("Danio rerio & Phascolarctos cinereus sequential, length 2, online", {
    df <- annotate_with_NCBI_taxid(
        c(7955, 38626),
        c("species", "phylum"),
        mode = "remote"
    )
    check <- c("Danio rerio", "Phascolarctos cinereus")
    df %>%
        dplyr::pull(species) %>%
        expect_setequal(check)
})

test_that("Danio rerio sequential all, online", {
    annotate_with_NCBI_taxid(7955, mode = "remote") %>%
        testthat::expect_snapshot()
})