tests/testthat/test-external_apis.R

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

context("external_apis")

test_that("geneNames: gene name query", {
    if (Sys.getenv("ONLINE_EXTERNAL_API") != "true") {
        local_mocked_bindings(
            useEnsembl = function(...) list(),
            getBM = function(...) {
                dplyr::tribble(
                    ~external_gene_name, ~ensembl_gene_id,
                    "MOB1A", "ENSG00000114978",
                    "TP53", "ENSG00000141510",
                    "SPIC", "ENSG00000166211",
                    "PTEN", "ENSG00000171862",
                    "RFLNB", "ENSG00000183688"
                )
            },
            .package = "biomaRt"
        )
    }

    target <- data.frame(
        ensembl = c(
            "ENSG00000114978",
            "ENSG00000166211",
            "ENSG00000183688",
            "ENSG00000171862",
            "ENSG00000141510"
        ),
        gene.name = c(
            "MOB1A",
            "SPIC",
            "RFLNB",
            "PTEN",
            "TP53"
        ),
        stringsAsFactors = FALSE,
        row.names = 1
    )

    geneNames(ensembl.genes = rownames(target)) |>
        lifecycle::expect_deprecated("ensemblGenes")
    geneNames(rownames(target), use.cache = TRUE) |>
        lifecycle::expect_deprecated("useCache")

    res <- geneNames(rownames(target))

    res$external_gene_name |>
        expect_equal(target[res$ensembl_gene_id, "gene.name"])
})

test_that("ensemblGeneNames: ensembl gene names query", {
    if (Sys.getenv("ONLINE_EXTERNAL_API") != "true") {
        local_mocked_bindings(
            useEnsembl = function(...) list(),
            getBM = function(...) {
                dplyr::tribble(
                    ~external_gene_name, ~ensembl_gene_id,
                    "MOB1A", "ENSG00000114978",
                    "TP53", "ENSG00000141510",
                    "SPIC", "ENSG00000166211",
                    "PTEN", "ENSG00000171862",
                    "RFLNB", "ENSG00000183688"
                )
            },
            .package = "biomaRt"
        )
    }

    target <- data.frame(
        ensembl = c(
            "ENSG00000114978",
            "ENSG00000166211",
            "ENSG00000183688",
            "ENSG00000171862",
            "ENSG00000141510"
        ),
        gene.name = c(
            "MOB1A",
            "SPIC",
            "RFLNB",
            "PTEN",
            "TP53"
        ),
        stringsAsFactors = FALSE,
        row.names = 2
    )

    ensemblGeneNames(gene.id = rownames(target)) |>
        lifecycle::expect_deprecated("geneId")
    ensemblGeneNames(rownames(target), use.cache = TRUE) |>
        lifecycle::expect_deprecated("useCache")

    res <- ensemblGeneNames(rownames(target))

    res$ensembl_gene_id |>
        expect_equal(target[res$external_gene_name, "ensembl"])
})

test_that("protein2EnsemblGeneNames: protein query", {
    if (Sys.getenv("ONLINE_EXTERNAL_API") != "true") {
        local_mocked_bindings(
            useEnsembl = function(...) list(),
            getBM = function(...) {
                dplyr::tribble(
                    ~ensembl_peptide_id, ~ensembl_gene_id,
                    "ENSP00000269305", "ENSG00000141510",
                    "ENSP00000331915", "ENSG00000183688",
                    "ENSP00000361021", "ENSG00000171862",
                    "ENSP00000379364", "ENSG00000114978"
                )
            },
            .package = "biomaRt"
        )
    }

    target <- data.frame(
        ensembl = c(
            "ENSP00000379364",
            "ENSP00000299272",
            "ENSP00000331915",
            "ENSP00000361021",
            "ENSP00000269305"
        ),
        gene.name = c(
            "ENSG00000114978",
            "ENSG00000166211",
            "ENSG00000183688",
            "ENSG00000171862",
            "ENSG00000141510"
        ),
        stringsAsFactors = FALSE,
        row.names = 1
    )

    protein2EnsemblGeneNames(ensembl.proteins = rownames(target)) |>
        lifecycle::expect_deprecated("ensemblProteins")
    protein2EnsemblGeneNames(rownames(target), use.cache = TRUE) |>
        lifecycle::expect_deprecated("useCache")

    res <- protein2EnsemblGeneNames(rownames(target))
    res$ensembl_gene_id |>
        expect_equal(target[res$ensembl_peptide_id, "gene.name"])
})

# test .curlWorkaround
test_that("curl workaround", {
    dummy <- function(...) rlang::abort("Expected error +1")

    aa <- .curlWorkaround(dummy()) |>
        expect_warning("calling the function with ssl_verifypeer to FALSE") |>
        expect_error("Expected error \\+1")
})

test_that("(all): connection fails", {
    local_mocked_bindings(
        useEnsembl = function(...) list(),
        getBM = function(...) {
            rlang::abort("Error no connection")
        },
        .package = "biomaRt"
    )

    genes <- c("MOB1A", "SPIC", "RFLNB", "PTEN", "TP53")

    res <- geneNames(genes) |>
        expect_warning("calling the function with ssl_verifypeer to FALSE")

    res$ensembl_gene_id |>
        expect_equal(res$external_gene_name)

    res <- ensemblGeneNames(genes) |>
        expect_warning("calling the function with ssl_verifypeer to FALSE")

    res$ensembl_gene_id |>
        expect_equal(res$external_gene_name)

    res <- protein2EnsemblGeneNames(genes) |>
        expect_warning("calling the function with ssl_verifypeer to FALSE")

    res$ensembl_gene_id |>
        expect_equal(res$external_gene_name)
})

test_that(".biomartLoad: handles error gracefully", {
    local_mocked_bindings(
        useEnsembl = function(...) list(),
        getBM = function(useCache = TRUE, ...) {
            if (isFALSE(useCache)) "success" else NULL
        },
        .package = "biomaRt"
    )

    result <- .biomartLoad(list(), list(), list(), useCache = TRUE, FALSE) |>
        expect_warning("calling the function with ssl_verifypeer to FALSE") |>
        expect_equal("success")
})