diff --git a/tests/testthat/test-ncbi_get_meta.R b/tests/testthat/test-ncbi_get_meta.R index d436209..b460278 100644 --- a/tests/testthat/test-ncbi_get_meta.R +++ b/tests/testthat/test-ncbi_get_meta.R @@ -4,7 +4,11 @@ test_that("ncbi_get_meta() works with history", { # with history, use history, one batch uids <- ncbi_get_uid("Microthrix parvicella", db = "biosample") meta <- suppressWarnings(ncbi_get_meta(uids)) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) # with history, use history, multiple batches uids <- ncbi_get_uid( @@ -13,8 +17,12 @@ test_that("ncbi_get_meta() works with history", { batch_size = 5 ) meta <- suppressWarnings(ncbi_get_meta(uids)) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) - expect_equal(nrow(meta), length(uids$uid)) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) + testthat::expect_equal(nrow(meta$main), length(uids$uid)) }) test_that("ncbi_get_meta() works without history", { @@ -25,14 +33,24 @@ test_that("ncbi_get_meta() works without history", { use_history = TRUE ) meta <- suppressWarnings(ncbi_get_meta(uids, use_history = FALSE)) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) + # with history, do not use history, multiple batches meta <- suppressWarnings(ncbi_get_meta( uids, use_history = FALSE, batch_size = 5 )) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) + # without history, attempt to use history but fall back, one batch uids <- ncbi_get_uid( "Microthrix parvicella", @@ -40,13 +58,21 @@ test_that("ncbi_get_meta() works without history", { use_history = FALSE ) meta <- suppressWarnings(ncbi_get_meta(uids)) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) # only ids, one batch meta <- suppressWarnings(ncbi_get_meta( uids$uid, db = "biosample" )) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) # only ids, multiple batches meta <- suppressWarnings(ncbi_get_meta( @@ -54,7 +80,11 @@ test_that("ncbi_get_meta() works without history", { db = "biosample", batch_size = 5 )) - expect_s3_class(meta, c("ncbi_meta", "tbl_df", "tbl", "data.frame")) + testthat::expect_true(inherits(meta, "list")) + testthat::expect_s3_class( + meta$main, + c("ncbi_meta", "tbl_df", "tbl", "data.frame") + ) }) test_that("ncbi_get_meta() works with all supported dbs", { diff --git a/tests/testthat/test-ncbi_parse.R b/tests/testthat/test-ncbi_parse.R index f5d5e5c..e836945 100644 --- a/tests/testthat/test-ncbi_parse.R +++ b/tests/testthat/test-ncbi_parse.R @@ -4,15 +4,20 @@ test_that("ncbi_parse() works with a BioSample", { data(examples) biosample_uid <- ncbi_get_uid(examples$biosample[1], db = "biosample") res <- ncbi_get_meta(biosample_uid) - expect_s3_class(res, c("tbl_df", "tbl", "data.frame")) - expect_equal(res$biosample, "SAMN02714232") + testthat::expect_true(inherits(res, "list")) + testthat::expect_s3_class(res$main, c("tbl_df", "tbl", "data.frame")) + expect_equal(res$main$biosample, "SAMN02714232") }) test_that("ncbi_parse() works with all BioSamples", { data(examples) biosample_uid <- ncbi_get_uid(examples$biosample, db = "biosample") res <- ncbi_get_meta(biosample_uid) - expect_s3_class(res, c("tbl_df", "tbl", "data.frame")) - expect_equal(nrow(res), length(examples$biosample)) + testthat::expect_true(inherits(res, "list")) + testthat::expect_equal(length(res), 2) + testthat::expect_equal(names(res), c("main", "antibiogram")) + testthat::expect_s3_class(res$main, c("tbl_df", "tbl", "data.frame")) + testthat::expect_s3_class(res$antibiogram, c("tbl_df", "tbl", "data.frame")) + expect_equal(nrow(res$main), length(examples$biosample)) })