context("Test: is.genome.available()") test_that("The is.genome.available() interface to NCBI RefSeq works properly..", { skip_on_cran() skip_on_travis() # test whether interface to 'refseq' works properly expect_equal(nrow(is.genome.available(db = "refseq", organism = "Saccharomyces cerevisiae", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "refseq", organism = "Saccharomyces cerevisiae", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to NCBI RefSeq works properly using taxid..", { skip_on_cran() skip_on_travis() # test whether interface to 'refseq' works properly expect_equal(nrow(is.genome.available(db = "refseq", organism = "559292", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "refseq", organism = "559292", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to NCBI RefSeq works properly using assembly accession id", { skip_on_cran() skip_on_travis() # test whether interface to 'refseq' works properly expect_equal(nrow(is.genome.available(db = "refseq", organism = "GCF_000146045.2", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "refseq", organism = "GCF_000146045.2", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to NCBI Genbank works properly..", { skip_on_cran() skip_on_travis() # test whether interface to 'genbank' works properly expect_equal(nrow(is.genome.available(db = "genbank", organism = "Saccharomyces cerevisiae", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "genbank", organism = "Saccharomyces cerevisiae", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to NCBI Genbank works properly using taxid..", { skip_on_cran() skip_on_travis() # test whether interface to 'genbank' works properly expect_equal(nrow(is.genome.available(db = "genbank", organism = "559292", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "genbank", organism = "559292", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to NCBI Genbank works properly using assembly accession id", { skip_on_cran() skip_on_travis() # test whether interface to 'genbank' works properly expect_equal(nrow(is.genome.available(db = "genbank", organism = "GCA_000091065.2", details = TRUE)) > 0, TRUE) # test whether it works properly a second time based on the internal files expect_equal(suppressMessages(is.genome.available(db = "genbank", organism = "GCA_000091065.2", details = FALSE)), TRUE) }) test_that("The is.genome.available() interface to Ensembl works properly..", { skip_on_cran() skip_on_travis() # test whether interface to 'ensembl' works properly expect_equal(nrow(is.genome.available(db = "ensembl", organism = "Saccharomyces cerevisiae", details = TRUE)) > 0, TRUE) # test whether interface to 'ensembl' works properly without details expect_equal(suppressMessages(is.genome.available(db = "ensembl", organism = "Saccharomyces cerevisiae")), TRUE) }) test_that("The is.genome.available() interface to Ensembl works properly using taxid..", { skip_on_cran() skip_on_travis() # test whether interface to 'ensembl' works properly expect_equal(nrow(is.genome.available(db = "ensembl", organism = "4932", details = TRUE)) > 0, TRUE) # test whether interface to 'ensembl' works properly without details expect_equal(suppressMessages(is.genome.available(db = "ensembl", organism = "4932")), TRUE) }) test_that("The is.genome.available() interface to Ensembl works properly using accession id", { skip_on_cran() skip_on_travis() # test whether interface to 'ensembl' works properly expect_equal(nrow(is.genome.available(db = "ensembl", organism = "GCA_000146045.2", details = TRUE)) > 0, TRUE) # test whether interface to 'ensembl' works properly without details expect_equal(suppressMessages(is.genome.available(db = "ensembl", organism = "GCA_000146045.2")), TRUE) }) test_that("The is.genome.available() error messages work properly..", { skip_on_cran() skip_on_travis() # test unknown organism error handling for 'refseq' expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "refseq")), FALSE) # test unknown organism error handling for 'genbank' expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "genbank")), FALSE) # test unknown organism error handling for 'ensembl' expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "ensembl")), FALSE) expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "uniprot")), FALSE) }) test_that("The is.genome.available() interface to Uniprot works properly..", { skip_on_cran() skip_on_travis() # test whether interface to 'uniprot' works properly out1 <- is.genome.available(db = "uniprot", organism = "Saccharomyces cerevisiae", details = TRUE) # test whether interface to 'uniprot' works properly without details out2 <- is.genome.available(db = "uniprot", organism = "Saccharomyces cerevisiae") expect_true(nrow(out1) > 0) expect_true(out2) })