Add tests for ncbi_get_meta() with dbs

R/ncbi_get_meta.R

@@ -104,6 +104,6 @@ ncbi_get_meta <- function(
     meta = res_parsed,
     web_history = if (use_history) uids$web_history else NULL
   )
-  class(out) <- c(paste("ncbi", db, "meta", sep = "_"), class(out))
+  class(out) <- c("ncbi_meta", class(out))
   return(out)
 }

R/ncbi_supported_dbs.R

@@ -1,6 +1,4 @@
 ncbi_supported_dbs <- function() {
-  dbs <- c(
-    "assembly", "bioproject", "biosample", "gene", "nuccore", "protein", "sra"
-  )
+  dbs <- c("assembly", "bioproject", "biosample", "gene", "protein", "sra")
   return(dbs)
 }

scripts/prep_examples.R

@@ -3,6 +3,7 @@ examples <- list(
     "GCF_000002435.2",
     "GCF_000299415.1"
   ),
+  bioproject = "PRJEB54063",
   biosample = c(
     "SAMN02714232", # contact email
     "SAMD00057211", # different ids, duplicated attributes
@@ -17,7 +18,10 @@ examples <- list(
     "SAMN00778252",
     "SAMEA3317914",
     "SAMEA14036741"
-  )
+  ),
+  gene = "948356",
+  protein = "AAA27507.1",
+  sra = "DRX061127"
 )
 
 save(examples, file = "data/examples.rda")

tests/testthat/test-ncbi_get_meta.R

@@ -1,7 +1,21 @@
 test_that("ncbi_get_meta() works with Microthrix parvicella", {
-  meta <- ncbi_get_meta("Microthrix parvicella", db = "biosample")
+  meta <- suppressWarnings(
+    ncbi_get_meta("Microthrix parvicella", db = "biosample")
+  )
   expect_s3_class(meta$meta, c("tbl_df", "tbl", "data.frame"))
 })
 
-
-
+test_that("ncbi_get_meta() works with all supported dbs", {
+  data(examples)
+
+  expect_true(all(names(examples) %in% ncbi_supported_dbs()))
+
+  for (i in names(examples)) {
+    res <- suppressWarnings(ncbi_get_meta(examples[[i]], db = i, parse = FALSE))
+
+    expect_true(all(class(res) == c("ncbi_meta", "list")))
+    expect_true("meta" %in% names(res))
+    expect_true(class(res$meta) == "list")
+    expect_true(class(res$meta[[1]]) == "character")
+  }
+})