tests/testthat/test-caching.R

In CshlSiepelLab/DENR: Deconvolution of Expression for Nascent RNA Sequencing Data

# Load in test txdb
txdb_path <- system.file("extdata", "hsapiens_gene_ensembl_96_txdb_test",
                        package = "DENR")
txdb <- AnnotationDbi::loadDb(file = txdb_path)
db_string <- "homo_sapiens-grch38.p12-ensembl_genes_96_test_Fh4Jf93l1.txdb"

test_that("Cache location can be set and retrieved", {
    cache_set_dir()
    expect_silent({
        cache_loc <- cache_get_dir()
    })
    expect_true(file.exists(cache_loc))
})

test_that("TxDb can be cached and retrieved", {
    cache_loc <- cache_get_dir()
    file_path <- paste0(file.path(cache_loc, db_string))
    expect_message(save_txdb(txdb = txdb,
                             annotation_version =
                                 "ensembl_genes_96_test_Fh4Jf93l1",
                             force = TRUE),
                   regexp = paste0("Saving db to ", file_path))
    expect_s4_class({
        txdb2 <<- load_txdb(db_string)},
                    class = "TxDb")
    AnnotationDbi::dbFileDisconnect(dbconn =  AnnotationDbi::dbconn(txdb2))
    # Force release of txdb file
    invisible(gc())
})

test_that("TxDb listed correctly", {
    expect_s3_class({
        txdb_list <- list_cached_txdb()},
                    "data.frame")
    expect_true(db_string %in% txdb_list$file_name)
})

test_that("view_available_txdb", {
    skip_if_offline(host = "www.ensembl.org")
    expect_s3_class(view_available_txdb("hsapiens", 98), "data.frame")
})